Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
In ApiDB 2.0 the federation has been implemented using Oracle DbLink technology.
[ "7" ]
80
11,300
0
false
In ApiDB 2.0 the federation has been implemented using Oracle DbLink technology.
[]
In ApiDB 2.0 the federation has been implemented using Oracle DbLink technology.
true
true
true
true
true
1,812
2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
In order to handle heterogeneous data sources in the future we are studying other federation approaches, such as Java Database Connectivity (JDBC) () and Web Services (WS) ().
[ "7" ]
175
11,301
0
false
In order to handle heterogeneous data sources in the future we are studying other federation approaches, such as Java Database Connectivity (JDBC) () and Web Services (WS) ().
[]
In order to handle heterogeneous data sources in the future we are studying other federation approaches, such as Java Database Connectivity (JDBC) () and Web Services (WS) ().
true
true
true
true
true
1,812
3
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b11", "b12" ]
17,098,930
pmid-10802651|pmid-10592242|pmid-9254694|pmid-16381887|pmid-16381885
ApiDB serves as a web portal for cross-species comparison.
[ "8", "9", "10", "11", "12" ]
58
11,302
0
false
ApiDB serves as a web portal for cross-species comparison.
[]
ApiDB serves as a web portal for cross-species comparison.
true
true
true
true
true
1,813
3
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b11", "b12" ]
17,098,930
pmid-10802651|pmid-10592242|pmid-9254694|pmid-16381887|pmid-16381885
Genome data from other apicomplexan parasites are also integrated.
[ "8", "9", "10", "11", "12" ]
66
11,303
0
false
Genome data from other apicomplexan parasites are also integrated.
[]
Genome data from other apicomplexan parasites are also integrated.
true
true
true
true
true
1,813
3
INTRODUCTION
1
8
[ "b8", "b9", "b10", "b11", "b12" ]
17,098,930
pmid-10802651|pmid-10592242|pmid-9254694|pmid-16381887|pmid-16381885
In its current release, ApiDB 2.0 offers an initial set of queries that enable gene searches of the three component databases by a variety of criteria such as text keywords, Enzyme Commission (EC) number Gene Ontology (8) assignments, and Pfam (9) terms.
[ "8", "9", "10", "11", "12" ]
254
11,304
1
false
In its current release, ApiDB 2.0 offers an initial set of queries that enable gene searches of the three component databases by a variety of criteria such as text keywords, Enzyme Commission (EC) number Gene Ontology assignments, and Pfam terms.
[ "8", "9" ]
In its current release, ApiDB 2.0 offers an initial set of queries that enable gene searches of the three component databases by a variety of criteria such as text keywords, Enzyme Commission (EC) number Gene Ontology assignments, and Pfam terms.
true
true
true
true
true
1,813
3
INTRODUCTION
1
10
[ "b8", "b9", "b10", "b11", "b12" ]
17,098,930
pmid-10802651|pmid-10592242|pmid-9254694|pmid-16381887|pmid-16381885
In addition, ApiDB offers tools to BLAST (10) all public apicomplexan data, access to the multi-species gene orthology database OrthoMCL DB (11) and access to KEGG (12) metabolic pathway maps with β€˜painted’ comparative highlights of apicomplexan and human enzymes.
[ "8", "9", "10", "11", "12" ]
264
11,305
1
false
In addition, ApiDB offers tools to BLAST all public apicomplexan data, access to the multi-species gene orthology database OrthoMCL DB and access to KEGG metabolic pathway maps with β€˜painted’ comparative highlights of apicomplexan and human enzymes.
[ "10", "11", "12" ]
In addition, ApiDB offers tools to BLAST all public apicomplexan data, access to the multi-species gene orthology database OrthoMCL DB and access to KEGG metabolic pathway maps with β€˜painted’ comparative highlights of apicomplexan and human enzymes.
true
true
true
true
true
1,813
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
The RecA family of proteins mediates homologous recombination, a ubiquitous mechanism for repairing DNA double strand breaks.
[ "1–3" ]
125
11,306
0
false
The RecA family of proteins mediates homologous recombination, a ubiquitous mechanism for repairing DNA double strand breaks.
[]
The RecA family of proteins mediates homologous recombination, a ubiquitous mechanism for repairing DNA double strand breaks.
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
Homologous recombination is involved in the recovery of collapsed DNA replication forks, in generating genetic diversity in meiosis and in establishing mitochondrial homoplasmy.
[ "1–3" ]
177
11,307
0
false
Homologous recombination is involved in the recovery of collapsed DNA replication forks, in generating genetic diversity in meiosis and in establishing mitochondrial homoplasmy.
[]
Homologous recombination is involved in the recovery of collapsed DNA replication forks, in generating genetic diversity in meiosis and in establishing mitochondrial homoplasmy.
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
Members of the RecA family include bacterial RecA, archaeal RadA or Rad51, eukaryotic Rad51 and meiosis-specific Dmc1.
[ "1–3" ]
118
11,308
0
false
Members of the RecA family include bacterial RecA, archaeal RadA or Rad51, eukaryotic Rad51 and meiosis-specific Dmc1.
[]
Members of the RecA family include bacterial RecA, archaeal RadA or Rad51, eukaryotic Rad51 and meiosis-specific Dmc1.
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
At double strand break sites, these proteins associate with single-stranded DNA (ssDNA) to form a right-handed helical nucleoprotein filament called the presynaptic complex.
[ "1–3" ]
173
11,309
0
false
At double strand break sites, these proteins associate with single-stranded DNA (ssDNA) to form a right-handed helical nucleoprotein filament called the presynaptic complex.
[]
At double strand break sites, these proteins associate with single-stranded DNA (ssDNA) to form a right-handed helical nucleoprotein filament called the presynaptic complex.
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
The presynaptic complex has both ATPase and DNA strand exchange activities: in the presence of Mg2+ and ATP, the DNA strand exchange activity ensures the formation of heteroduplex DNA (hDNA) between ssDNA and its complementary strand in the double-stranded DNA (dsDNA).
[ "1–3" ]
269
11,310
0
false
The presynaptic complex has both ATPase and DNA strand exchange activities: in the presence of Mg2+ and ATP, the DNA strand exchange activity ensures the formation of heteroduplex DNA (hDNA) between ssDNA and its complementary strand in the double-stranded DNA (dsDNA).
[]
The presynaptic complex has both ATPase and DNA strand exchange activities: in the presence of Mg2+ and ATP, the DNA strand exchange activity ensures the formation of heteroduplex DNA (hDNA) between ssDNA and its complementary strand in the double-stranded DNA (dsDNA).
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
The hDNA formation can be conveniently monitored and quantified on an agarose gel using the D-loop formation assay.
[ "1–3" ]
115
11,311
0
false
The hDNA formation can be conveniently monitored and quantified on an agarose gel using the D-loop formation assay.
[]
The hDNA formation can be conveniently monitored and quantified on an agarose gel using the D-loop formation assay.
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
The molecular mechanism underlying the rather slow DNA-dependent ATPase activity is still not clear.
[ "1–3" ]
100
11,312
0
false
The molecular mechanism underlying the rather slow DNA-dependent ATPase activity is still not clear.
[]
The molecular mechanism underlying the rather slow DNA-dependent ATPase activity is still not clear.
true
true
true
true
true
1,814
0
INTRODUCTION
1
1–3
[ "B1 B2 B3" ]
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
It has been proposed that ATP hydrolysis promotes product release, recycling of recombinase monomers and/or a rotary mechanism that could relieve the DNA topological problem in the strand exchange reaction (1–3).
[ "1–3" ]
212
11,313
1
false
It has been proposed that ATP hydrolysis promotes product release, recycling of recombinase monomers and/or a rotary mechanism that could relieve the DNA topological problem in the strand exchange reaction.
[ "1–3" ]
It has been proposed that ATP hydrolysis promotes product release, recycling of recombinase monomers and/or a rotary mechanism that could relieve the DNA topological problem in the strand exchange reaction.
true
true
true
true
true
1,814
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
Members of the RecA family share a core ATPase domain containing the putative ssDNA binding motifs, the L1 and L2 loops (4).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
124
11,314
1
false
Members of the RecA family share a core ATPase domain containing the putative ssDNA binding motifs, the L1 and L2 loops.
[ "4" ]
Members of the RecA family share a core ATPase domain containing the putative ssDNA binding motifs, the L1 and L2 loops.
true
true
true
true
true
1,815
1
INTRODUCTION
1
5
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
The ATPase domain is preceded by a short Ξ²-strand polymerization motif (5).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
75
11,315
1
false
The ATPase domain is preceded by a short Ξ²-strand polymerization motif.
[ "5" ]
The ATPase domain is preceded by a short Ξ²-strand polymerization motif.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
RadA, Rad51 and Dmc1 have an additional, smaller N-terminal domain (NTD) that may interact with dsDNA (6,7), whereas RecA has a small C-terminal domain with a similar proposed function.
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
185
11,316
0
false
RadA, Rad51 and Dmc1 have an additional, smaller N-terminal domain (NTD) that may interact with dsDNA, whereas RecA has a small C-terminal domain with a similar proposed function.
[ "6,7" ]
RadA, Rad51 and Dmc1 have an additional, smaller N-terminal domain (NTD) that may interact with dsDNA, whereas RecA has a small C-terminal domain with a similar proposed function.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
The helix-hairpin-helix (HhH) motif in the NTD (Figure 1) mediates dsDNA
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
72
11,317
0
false
The helix-hairpin-helix (HhH) motif in the NTD (Figure 1) mediates dsDNA
[]
The helix-hairpin-helix (HhH) motif in the NTD (Figure 1) mediates dsDNA
true
true
false
true
false
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
binding (6,7).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
14
11,318
0
false
binding.
[ "6,7" ]
binding.
false
true
true
true
false
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
The crystal structures of several RecA family members have revealed that the polymerization motif is responsible for assembly of helical filaments and toroidal rings (4,8–13).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
175
11,319
0
false
The crystal structures of several RecA family members have revealed that the polymerization motif is responsible for assembly of helical filaments and toroidal rings.
[ "4,8–13" ]
The crystal structures of several RecA family members have revealed that the polymerization motif is responsible for assembly of helical filaments and toroidal rings.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
A hydrophobic residue (phenylalanine in RadA, Rad51 and Dmc1, and isoleucine in RecA) in the polymerization motif docks into a hydrophobic pocket on the neighbouring core ATPase domain.
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
185
11,320
0
false
A hydrophobic residue in the polymerization motif docks into a hydrophobic pocket on the neighbouring core ATPase domain.
[ "phenylalanine in RadA, Rad51 and Dmc1, and isoleucine in RecA" ]
A hydrophobic residue in the polymerization motif docks into a hydrophobic pocket on the neighbouring core ATPase domain.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
This interaction was also observed in the structure of a fusion construct combining the human Rad51 monomer and a peptide from BRCA2 (5,8).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
139
11,321
0
false
This interaction was also observed in the structure of a fusion construct combining the human Rad51 monomer and a peptide from BRCA2.
[ "5,8" ]
This interaction was also observed in the structure of a fusion construct combining the human Rad51 monomer and a peptide from BRCA2.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
Figure 1.Sequence alignment of RecA family proteins from S.solfataricus (Sso RadA), M.voltae (MvRadA), P.furiosus (PfRad51), H.sapiens (HsRad51 and HsDmc1), S.cerevisiae (ScDmc1 and ScRad51) and E.coli (EcRecA).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
211
11,322
0
false
Figure 1.Sequence alignment of RecA family proteins from S.solfataricus (Sso RadA), M.voltae (MvRadA), P.furiosus, H.sapiens, S.cerevisiae and E.coli (EcRecA).
[ "PfRad51", "HsRad51 and HsDmc1", "ScDmc1 and ScRad51" ]
Figure 1.Sequence alignment of RecA family proteins from S.solfataricus (Sso RadA), M.voltae (MvRadA), P.furiosus, H.sapiens, S.cerevisiae and E.coli (EcRecA).
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
All these RecA-like strand exchange proteins have similar N-terminal domains.
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
77
11,323
0
false
All these RecA-like strand exchange proteins have similar N-terminal domains.
[]
All these RecA-like strand exchange proteins have similar N-terminal domains.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
The C-terminal RecA domains have been removed for clarity.
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
58
11,324
0
false
The C-terminal RecA domains have been removed for clarity.
[]
The C-terminal RecA domains have been removed for clarity.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
Secondary structural features of the left-handed SsoRadA helical filament are indicated in cyan (Ξ± helices) and red (Ξ² strands).
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
128
11,325
0
false
Secondary structural features of the left-handed SsoRadA helical filament are indicated in cyan (Ξ± helices) and red (Ξ² strands).
[]
Secondary structural features of the left-handed SsoRadA helical filament are indicated in cyan (Ξ± helices) and red (Ξ² strands).
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
Functional motifs are indicated under their corresponding amino acid sequences: the putative dsDNA binding HhH motif, the putative ssDNA binding L1 and L2 loops, the ATP binding Walker A and B motifs, the polymerization motif (PM), the subunit rotation motif (SRM), and others.
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
277
11,326
0
false
Functional motifs are indicated under their corresponding amino acid sequences: the putative dsDNA binding HhH motif, the putative ssDNA binding L1 and L2 loops, the ATP binding Walker A and B motifs, the polymerization motif (PM), the subunit rotation motif (SRM), and others.
[]
Functional motifs are indicated under their corresponding amino acid sequences: the putative dsDNA binding HhH motif, the putative ssDNA binding L1 and L2 loops, the ATP binding Walker A and B motifs, the polymerization motif (PM), the subunit rotation motif (SRM), and others.
true
true
true
true
true
1,815
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B6", "B7", "B4", "B8 B9 B10 B11 B12 B13", "B5", "B8" ]
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
Positions of the R0–E1–E2 triad are indicated using blue arrows.
[ "4", "5", "6", "7", "6", "7", "4", "8–13", "5", "8" ]
64
11,327
0
false
Positions of the R0–E1–E2 triad are indicated using blue arrows.
[]
Positions of the R0–E1–E2 triad are indicated using blue arrows.
true
true
true
true
true
1,815
2
INTRODUCTION
0
null
null
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
Sequence alignment of RecA family proteins from S.solfataricus (Sso RadA), M.voltae (MvRadA), P.furiosus (PfRad51), H.sapiens (HsRad51 and HsDmc1), S.cerevisiae (ScDmc1 and ScRad51) and E.coli (EcRecA).
null
202
11,328
0
false
null
null
Sequence alignment of RecA family proteins from S.solfataricus (Sso RadA), M.voltae (MvRadA), P.furiosus (PfRad51), H.sapiens (HsRad51 and HsDmc1), S.cerevisiae (ScDmc1 and ScRad51) and E.coli (EcRecA).
true
true
true
true
true
1,816
2
INTRODUCTION
0
null
null
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
All these RecA-like strand exchange proteins have similar N-terminal domains.
null
77
11,329
0
false
null
null
All these RecA-like strand exchange proteins have similar N-terminal domains.
true
true
true
true
true
1,816
2
INTRODUCTION
0
null
null
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
The C-terminal RecA domains have been removed for clarity.
null
58
11,330
0
false
null
null
The C-terminal RecA domains have been removed for clarity.
true
true
true
true
true
1,816
2
INTRODUCTION
0
null
null
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
Secondary structural features of the left-handed SsoRadA helical filament are indicated in cyan (Ξ± helices) and red (Ξ² strands).
null
128
11,331
0
false
null
null
Secondary structural features of the left-handed SsoRadA helical filament are indicated in cyan (Ξ± helices) and red (Ξ² strands).
true
true
true
true
true
1,816
2
INTRODUCTION
0
null
null
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
Functional motifs are indicated under their corresponding amino acid sequences: the putative dsDNA binding HhH motif, the putative ssDNA binding L1 and L2 loops, the ATP binding Walker A and B motifs, the polymerization motif (PM), the subunit rotation motif (SRM), and others.
null
277
11,332
0
false
null
null
Functional motifs are indicated under their corresponding amino acid sequences: the putative dsDNA binding HhH motif, the putative ssDNA binding L1 and L2 loops, the ATP binding Walker A and B motifs, the polymerization motif (PM), the subunit rotation motif (SRM), and others.
true
true
true
true
true
1,816
2
INTRODUCTION
0
null
null
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
Positions of the R0–E1–E2 triad are indicated using blue arrows.
null
64
11,333
0
false
null
null
Positions of the R0–E1–E2 triad are indicated using blue arrows.
true
true
true
true
true
1,816
3
INTRODUCTION
1
11
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
For RecA proteins, the transition from closed rings to helical filaments could be flexible or regulated.
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
104
11,334
0
false
For RecA proteins, the transition from closed rings to helical filaments could be flexible or regulated.
[]
For RecA proteins, the transition from closed rings to helical filaments could be flexible or regulated.
true
true
true
true
true
1,817
3
INTRODUCTION
1
11
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Archaeal RadA proteins form both closed rings and right-handed helical filaments (11,13–16).
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
92
11,335
0
false
Archaeal RadA proteins form both closed rings and right-handed helical filaments.
[ "11,13–16" ]
Archaeal RadA proteins form both closed rings and right-handed helical filaments.
true
true
true
true
true
1,817
3
INTRODUCTION
1
17–19
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Saccharomyces cerevisiae Dmc1 (ScDmc1) and human Dmc1 proteins, in the presence of ssDNA, switch from rings to helical filaments in a Ca2+-dependent manner (17–19).
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
164
11,336
1
false
Saccharomyces cerevisiae Dmc1 (ScDmc1) and human Dmc1 proteins, in the presence of ssDNA, switch from rings to helical filaments in a Ca2+-dependent manner.
[ "17–19" ]
Saccharomyces cerevisiae Dmc1 and human Dmc1 proteins, in the presence of ssDNA, switch from rings to helical filaments in a Ca2+-dependent manner.
true
true
true
true
true
1,817
3
INTRODUCTION
1
11
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Conceivably, all members of the RecA family form similar right-handed nucleoprotein filaments in which the ssDNA lies close to the filament axis.
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
145
11,337
0
false
Conceivably, all members of the RecA family form similar right-handed nucleoprotein filaments in which the ssDNA lies close to the filament axis.
[]
Conceivably, all members of the RecA family form similar right-handed nucleoprotein filaments in which the ssDNA lies close to the filament axis.
true
true
true
true
true
1,817
3
INTRODUCTION
1
11
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
These nucleoprotein filaments are thought to be catalytically active in mediating strand exchange reactions (14,15,17–20).
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
122
11,338
0
false
These nucleoprotein filaments are thought to be catalytically active in mediating strand exchange reactions.
[ "14,15,17–20" ]
These nucleoprotein filaments are thought to be catalytically active in mediating strand exchange reactions.
true
true
true
true
true
1,817
3
INTRODUCTION
1
11
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
In this study, we report that both Sulfolobus solfataricus (Sso) RadA and ScDmc1 can exist as left-handed filaments.
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
116
11,339
0
false
In this study, we report that both Sulfolobus solfataricus (Sso) RadA and ScDmc1 can exist as left-handed filaments.
[]
In this study, we report that both Sulfolobus solfataricus (Sso) RadA and ScDmc1 can exist as left-handed filaments.
true
true
true
true
true
1,817
3
INTRODUCTION
1
11
[ "B11", "B13 B14 B15 B16", "B17 B18 B19", "B14", "B15", "B17 B18 B19 B20" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Using a structure-based approach, we studied the assembly mechanism and functional relevance of the SsoRadA left-handed protein filament.
[ "11", "13–16", "17–19", "14", "15", "17–20" ]
137
11,340
0
false
Using a structure-based approach, we studied the assembly mechanism and functional relevance of the SsoRadA left-handed protein filament.
[]
Using a structure-based approach, we studied the assembly mechanism and functional relevance of the SsoRadA left-handed protein filament.
true
true
true
true
true
1,817
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
In summary, we report that members of the RecA protein family can self-polymerize into left-handed helical filaments in vitro.
null
126
11,341
0
false
null
null
In summary, we report that members of the RecA protein family can self-polymerize into left-handed helical filaments in vitro.
true
true
true
true
true
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
Subsequent structural and functional analysis led to the identification of a new functional motif, the SRM, in this protein family.
null
131
11,342
0
false
null
null
Subsequent structural and functional analysis led to the identification of a new functional motif, the SRM, in this protein family.
true
true
true
true
true
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
We favor the notion that axial rotation of the SRMs may control not only the quaternary structures of RecA family proteins (at least in protein crystals), but also regulate their enzymatic functions.
null
199
11,343
0
false
null
null
We favor the notion that axial rotation of the SRMs may control not only the quaternary structures of RecA family proteins (at least in protein crystals), but also regulate their enzymatic functions.
true
true
true
true
true
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
We speculate that the left-handed helical filament, if it forms in a physiological context, may stabilize hDNA at the end of the DNA strand assimilation reaction.
null
162
11,344
0
false
null
null
We speculate that the left-handed helical filament, if it forms in a physiological context, may stabilize hDNA at the end of the DNA strand assimilation reaction.
true
true
true
true
true
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
Since the left-handed helical filament tends to exclude ssDNA, it may also represent a conformation for uncoupling RecA family proteins from ssDNA when the latter fails to find a homologous dsDNA partner to complete the DNA strand assimilation reaction.
null
253
11,345
0
false
null
null
Since the left-handed helical filament tends to exclude ssDNA, it may also represent a conformation for uncoupling RecA family proteins from ssDNA when the latter fails to find a homologous dsDNA partner to complete the DNA strand assimilation reaction.
true
true
true
true
true
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
In both scenarios, i.e.
null
23
11,346
0
false
null
null
In both scenarios, i.e.
true
true
true
true
true
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
hDNA stabilization and ssDNA exclusion, the left-handed helical filament may represent an intermediate during or after the strand assimilation reaction.
null
152
11,347
0
false
null
null
hDNA stabilization and ssDNA exclusion, the left-handed helical filament may represent an intermediate during or after the strand assimilation reaction.
false
true
true
true
false
1,818
0
DISCUSSION
0
null
null
17,329,376
pmid-7979259|pmid-12778123|pmid-14527291
This supposition is consistent with our findings that left-handed filaments were more often observed when the wild-type SsoRadA protein was incubated with the reaction buffer for D-loop formation (Figure 2).
null
207
11,348
0
false
null
null
This supposition is consistent with our findings that left-handed filaments were more often observed when the wild-type SsoRadA protein was incubated with the reaction buffer for D-loop formation (Figure 2).
true
true
true
true
true
1,818
1
DISCUSSION
0
null
null
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
However, we have yet to obtain indisputable evidence confirming that the left-handed helical filament is involved in the strand exchange reaction.
null
146
11,349
0
false
null
null
However, we have yet to obtain indisputable evidence confirming that the left-handed helical filament is involved in the strand exchange reaction.
true
true
true
true
true
1,819
1
DISCUSSION
0
null
null
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
It may be critical to identify a mutant defective in left-handed filament formation.
null
84
11,350
0
false
null
null
It may be critical to identify a mutant defective in left-handed filament formation.
true
true
true
true
true
1,819
1
DISCUSSION
0
null
null
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
It would be interesting to determine if the R83A proteins only form left-handed filaments and if the N85P proteins only form right-handed filaments.
null
148
11,351
0
false
null
null
It would be interesting to determine if the R83A proteins only form left-handed filaments and if the N85P proteins only form right-handed filaments.
true
true
true
true
true
1,819
1
DISCUSSION
0
null
null
17,329,376
pmid-1731253|pmid-12442171|pmid-10390347|pmid-15917243|pmid-10390347|pmid-15917243|pmid-1731253|pmid-12941707|pmid-15125839|pmid-15235592|pmid-15304222|pmid-16229465|pmid-15755748|pmid-12442171|pmid-12941707
Alternatively, the SRM may be flexible enough to promote the strand exchange reaction by adapting alternative conformations or structural intermediates.
null
152
11,352
0
false
null
null
Alternatively, the SRM may be flexible enough to promote the strand exchange reaction by adapting alternative conformations or structural intermediates.
true
true
true
true
true
1,819
2
DISCUSSION
1
30
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
The biochemistry data in this report suggests that SRM is important for coupling SsoRadA's ssDNA binding and ATPase activities to its strand exchange activity.
[ "30", "31", "12" ]
159
11,353
0
false
The biochemistry data in this report suggests that SRM is important for coupling SsoRadA's ssDNA binding and ATPase activities to its strand exchange activity.
[]
The biochemistry data in this report suggests that SRM is important for coupling SsoRadA's ssDNA binding and ATPase activities to its strand exchange activity.
true
true
true
true
true
1,820
2
DISCUSSION
1
30
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
Similar to the rotary motor F1-ATPase, the use of ATP in SsoRadA might involve three sequential states: an ATP-bound state (TP), an intermediate (DP), and a state in which the nucleotide binding site is empty (E) (30).
[ "30", "31", "12" ]
218
11,354
1
false
Similar to the rotary motor F1-ATPase, the use of ATP in SsoRadA might involve three sequential states: an ATP-bound state (TP), an intermediate (DP), and a state in which the nucleotide binding site is empty (E).
[ "30" ]
Similar to the rotary motor F1-ATPase, the use of ATP in SsoRadA might involve three sequential states: an ATP-bound state (TP), an intermediate (DP), and a state in which the nucleotide binding site is empty (E).
true
true
true
true
true
1,820
2
DISCUSSION
1
30
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
The R83A and N85P point mutants may carry out the TP to DP transition, but are incapable of transmitting these allosteric effects to strand assimilation or exchange.
[ "30", "31", "12" ]
165
11,355
0
false
The R83A and N85P point mutants may carry out the TP to DP transition, but are incapable of transmitting these allosteric effects to strand assimilation or exchange.
[]
The R83A and N85P point mutants may carry out the TP to DP transition, but are incapable of transmitting these allosteric effects to strand assimilation or exchange.
true
true
true
true
true
1,820
2
DISCUSSION
1
30
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
On the other hand, the R83E point mutant may be defective in the transition from E to TP.
[ "30", "31", "12" ]
89
11,356
0
false
On the other hand, the R83E point mutant may be defective in the transition from E to TP.
[]
On the other hand, the R83E point mutant may be defective in the transition from E to TP.
true
true
true
true
true
1,820
2
DISCUSSION
1
30
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
Accordingly, the SRM may control the TP-DP-E transition.
[ "30", "31", "12" ]
56
11,357
0
false
Accordingly, the SRM may control the TP-DP-E transition.
[]
Accordingly, the SRM may control the TP-DP-E transition.
true
true
true
true
true
1,820
2
DISCUSSION
1
31
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
This model is consistent with a previous report that the use of ATP in E.coli RecA occurs sequentially in three steps (31).
[ "30", "31", "12" ]
123
11,358
1
false
This model is consistent with a previous report that the use of ATP in E.coli RecA occurs sequentially in three steps.
[ "31" ]
This model is consistent with a previous report that the use of ATP in E.coli RecA occurs sequentially in three steps.
true
true
true
true
true
1,820
2
DISCUSSION
1
12
[ "B30", "B31", "B12" ]
17,329,376
pmid-11509182|pmid-3981638|pmid-16229465
In addition, a recent study indicated that the transition from TP to DP by MvRadA involved extensive allosteric effects spanning the ATPase site and the L2 putative DNA-binding loop (12).
[ "30", "31", "12" ]
187
11,359
1
false
In addition, a recent study indicated that the transition from TP to DP by MvRadA involved extensive allosteric effects spanning the ATPase site and the L2 putative DNA-binding loop.
[ "12" ]
In addition, a recent study indicated that the transition from TP to DP by MvRadA involved extensive allosteric effects spanning the ATPase site and the L2 putative DNA-binding loop.
true
true
true
true
true
1,820
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Another important finding in this report is that the R0 of the SRM is evolutionarily conserved in almost all RecA family proteins, including archaeal RadA and Rad51, eukaryotic Rad51 and Dmc1 and E.coli RecA (Figure 1).
[ "10", "29", "32", "28", "34", "3" ]
219
11,360
0
false
Another important finding in this report is that the R0 of the SRM is evolutionarily conserved in almost all RecA family proteins, including archaeal RadA and Rad51, eukaryotic Rad51 and Dmc1 and E.coli RecA (Figure 1).
[]
Another important finding in this report is that the R0 of the SRM is evolutionarily conserved in almost all RecA family proteins, including archaeal RadA and Rad51, eukaryotic Rad51 and Dmc1 and E.coli RecA.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Arg34, the R0 of E.coli RecA, is also located immediately after a single Ξ²-strand which functions as the polymerization motif (Ile27) for RecA filament assembly (10).
[ "10", "29", "32", "28", "34", "3" ]
166
11,361
1
false
Arg34, the R0 of E.coli RecA, is also located immediately after a single Ξ²-strand which functions as the polymerization motif (Ile27) for RecA filament assembly.
[ "10" ]
Arg34, the R0 of E.coli RecA, is also located immediately after a single Ξ²-strand which functions as the polymerization motif (Ile27) for RecA filament assembly.
true
true
true
true
true
1,821
3
DISCUSSION
1
29
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
The polymerization motif of the E.coli RecA protein resides between its small NTD (amino acid residues 1–22) and the core ATPase domain (amino acid residues 36–353) (29).
[ "10", "29", "32", "28", "34", "3" ]
170
11,362
1
false
The polymerization motif of the E.coli RecA protein resides between its small NTD (amino acid residues 1–22) and the core ATPase domain.
[ "amino acid residues 36–353", "29" ]
The polymerization motif of the E.coli RecA protein resides between its small NTD and the core ATPase domain.
true
true
true
true
true
1,821
3
DISCUSSION
1
32
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
A recent structural study reported that changes in the dihedral angles of two amino acid (Lys23 and Gly24) residing in the polymerization motif were responsible for rotation of the RecA filament between compressed and stretched conformations (32).
[ "10", "29", "32", "28", "34", "3" ]
247
11,363
1
false
A recent structural study reported that changes in the dihedral angles of two amino acid residing in the polymerization motif were responsible for rotation of the RecA filament between compressed and stretched conformations.
[ "Lys23 and Gly24", "32" ]
A recent structural study reported that changes in the dihedral angles of two amino acid residing in the polymerization motif were responsible for rotation of the RecA filament between compressed and stretched conformations.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
We noticed that Arg34 formed a salt bridge with Glu19 in a compressed RecA helical filament (74 Å helical pitch; 33), and this salt bridge fell apart in a relaxed RecA helical filament (83 Å helical pitch; 29) (Figure 10).
[ "10", "29", "32", "28", "34", "3" ]
222
11,364
0
false
We noticed that Arg34 formed a salt bridge with Glu19 in a compressed RecA helical filament, and this salt bridge fell apart in a relaxed RecA helical filament.
[ "74 Å helical pitch; 33", "83 Å helical pitch; 29", "Figure 10" ]
We noticed that Arg34 formed a salt bridge with Glu19 in a compressed RecA helical filament, and this salt bridge fell apart in a relaxed RecA helical filament.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Accordingly, this Arg34–Glu19 dyad may be functionally similar to the E1–R0–E2 triads of the archaeal and eukaryotic proteins.
[ "10", "29", "32", "28", "34", "3" ]
126
11,365
0
false
Accordingly, this Arg34–Glu19 dyad may be functionally similar to the E1–R0–E2 triads of the archaeal and eukaryotic proteins.
[]
Accordingly, this Arg34–Glu19 dyad may be functionally similar to the E1–R0–E2 triads of the archaeal and eukaryotic proteins.
true
true
true
true
true
1,821
3
DISCUSSION
1
28
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
It would be interesting to determine whether Arg34 or Glu19 is essential for RecA enzymatic activity, or for RecA to form left-handed nucleoprotein filaments (28).
[ "10", "29", "32", "28", "34", "3" ]
163
11,366
1
false
It would be interesting to determine whether Arg34 or Glu19 is essential for RecA enzymatic activity, or for RecA to form left-handed nucleoprotein filaments.
[ "28" ]
It would be interesting to determine whether Arg34 or Glu19 is essential for RecA enzymatic activity, or for RecA to form left-handed nucleoprotein filaments.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Conservation of R0 in all RecA family proteins also indicates that the SRM does not simply function as a flexible inter-domain linker.
[ "10", "29", "32", "28", "34", "3" ]
134
11,367
0
false
Conservation of R0 in all RecA family proteins also indicates that the SRM does not simply function as a flexible inter-domain linker.
[]
Conservation of R0 in all RecA family proteins also indicates that the SRM does not simply function as a flexible inter-domain linker.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
This is consistent with our findings that the R83E mutant is defective in ssDNA-stimulated ATPase activity and that the R83A and R83E mutants are defective in the strand exchange reaction.
[ "10", "29", "32", "28", "34", "3" ]
188
11,368
0
false
This is consistent with our findings that the R83E mutant is defective in ssDNA-stimulated ATPase activity and that the R83A and R83E mutants are defective in the strand exchange reaction.
[]
This is consistent with our findings that the R83E mutant is defective in ssDNA-stimulated ATPase activity and that the R83A and R83E mutants are defective in the strand exchange reaction.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Therefore, R0 may be directly involved in coupling ATP hydrolysis to the strand exchange reaction.
[ "10", "29", "32", "28", "34", "3" ]
98
11,369
0
false
Therefore, R0 may be directly involved in coupling ATP hydrolysis to the strand exchange reaction.
[]
Therefore, R0 may be directly involved in coupling ATP hydrolysis to the strand exchange reaction.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
In this scenario, R0 is functionally similar to Arg242 in the E.coli F1F0 ATPase Ξ³ subunit.
[ "10", "29", "32", "28", "34", "3" ]
91
11,370
0
false
In this scenario, R0 is functionally similar to Arg242 in the E.coli F1F0 ATPase Ξ³ subunit.
[]
In this scenario, R0 is functionally similar to Arg242 in the E.coli F1F0 ATPase Ξ³ subunit.
true
true
true
true
true
1,821
3
DISCUSSION
1
34
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Arg242 forms a salt-bridge with Glu381 of the catalytic Ξ²DP subunit, and this β–γ interaction plays an important role in turnover and coupling (34).
[ "10", "29", "32", "28", "34", "3" ]
148
11,371
1
false
Arg242 forms a salt-bridge with Glu381 of the catalytic Ξ²DP subunit, and this β–γ interaction plays an important role in turnover and coupling.
[ "34" ]
Arg242 forms a salt-bridge with Glu381 of the catalytic Ξ²DP subunit, and this β–γ interaction plays an important role in turnover and coupling.
true
true
true
true
true
1,821
3
DISCUSSION
1
3
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Intriguingly, a rotary motor model had been proposed for RecA family proteins to explain the coupling of ATP hydrolysis to DNA strand exchange activity (3).
[ "10", "29", "32", "28", "34", "3" ]
156
11,372
1
false
Intriguingly, a rotary motor model had been proposed for RecA family proteins to explain the coupling of ATP hydrolysis to DNA strand exchange activity.
[ "3" ]
Intriguingly, a rotary motor model had been proposed for RecA family proteins to explain the coupling of ATP hydrolysis to DNA strand exchange activity.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Since the comparative structural analysis in this report (Figure 5) led to the speculation that the SRM may be flexible enough to allow the archaeal RadA and Rad51 protein filaments to rotate 360Β°, we propose the following rotary motor model for RadA or Rad51 proteins (Figure 11).
[ "10", "29", "32", "28", "34", "3" ]
281
11,373
0
false
Since the comparative structural analysis in this report (Figure 5) led to the speculation that the SRM may be flexible enough to allow the archaeal RadA and Rad51 protein filaments to rotate 360Β°, we propose the following rotary motor model for RadA or Rad51 proteins (Figure 11).
[]
Since the comparative structural analysis in this report (Figure 5) led to the speculation that the SRM may be flexible enough to allow the archaeal RadA and Rad51 protein filaments to rotate 360Β°, we propose the following rotary motor model for RadA or Rad51 proteins.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
First, RadA/Rad51 proteins exist as protein rings in the resting state (left panel).
[ "10", "29", "32", "28", "34", "3" ]
84
11,374
0
false
First, RadA/Rad51 proteins exist as protein rings in the resting state (left panel).
[]
First, RadA/Rad51 proteins exist as protein rings in the resting state (left panel).
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
After association with ATP or AMP–PNP, the RadA proteins form a P61 right-handed helical filament, which represents the TP intermediate state.
[ "10", "29", "32", "28", "34", "3" ]
142
11,375
0
false
After association with ATP or AMP–PNP, the RadA proteins form a P61 right-handed helical filament, which represents the TP intermediate state.
[]
After association with ATP or AMP–PNP, the RadA proteins form a P61 right-handed helical filament, which represents the TP intermediate state.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Second, ssDNA binding induces ATP hydrolysis (by disrupting the E1–Ro–E2 triad and slightly widening the ATP binding pocket) in conjunction with an ∼120Β° axial rotation into the P31 overwound right-handed filament.
[ "10", "29", "32", "28", "34", "3" ]
214
11,376
0
false
Second, ssDNA binding induces ATP hydrolysis (by disrupting the E1–Ro–E2 triad and slightly widening the ATP binding pocket) in conjunction with an ∼120Β° axial rotation into the P31 overwound right-handed filament.
[]
Second, ssDNA binding induces ATP hydrolysis in conjunction with an ∼120° axial rotation into the P31 overwound right-handed filament.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
This overwound right-handed filament may represent or resemble the DP intermediate state.
[ "10", "29", "32", "28", "34", "3" ]
89
11,377
0
false
This overwound right-handed filament may represent or resemble the DP intermediate state.
[]
This overwound right-handed filament may represent or resemble the DP intermediate state.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Intriguingly, the P61 to P31 structural transition is accompanied by concerted movements of the L1, L2 and HhH motifs from filament centre to filament surface.
[ "10", "29", "32", "28", "34", "3" ]
159
11,378
0
false
Intriguingly, the P61 to P31 structural transition is accompanied by concerted movements of the L1, L2 and HhH motifs from filament centre to filament surface.
[]
Intriguingly, the P61 to P31 structural transition is accompanied by concerted movements of the L1, L2 and HhH motifs from filament centre to filament surface.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Together, these three DNA binding motifs constitute a 25 Å open pocket (L.-T. Chen et al., unpublished results) that is wide enough to capture dsDNA and mediate homologous pairing between ssDNA and dsDNA.
[ "10", "29", "32", "28", "34", "3" ]
204
11,379
0
false
Together, these three DNA binding motifs constitute a 25 Γ… open pocket (L.-T. Chen et al., unpublished results) that is wide enough to capture dsDNA and mediate homologous pairing between ssDNA and dsDNA.
[]
Together, these three DNA binding motifs constitute a 25 Γ… open pocket (L.-T. Chen et al., unpublished results) that is wide enough to capture dsDNA and mediate homologous pairing between ssDNA and dsDNA.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Third, release of ADP and inorganic phosphate (Pi) induces an additional ∼120° axial rotation and results into the P43 left-handed helical filament or the E intermediate state, because the ATP binding pocket of the left-handed filament is wide open.
[ "10", "29", "32", "28", "34", "3" ]
249
11,380
0
false
Third, release of ADP and inorganic phosphate (Pi) induces an additional ∼120° axial rotation and results into the P43 left-handed helical filament or the E intermediate state, because the ATP binding pocket of the left-handed filament is wide open.
[]
Third, release of ADP and inorganic phosphate (Pi) induces an additional ∼120° axial rotation and results into the P43 left-handed helical filament or the E intermediate state, because the ATP binding pocket of the left-handed filament is wide open.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
The strand exchange reaction between ssDNA and dsDNA likely occurs during this structural transition, since the HhH dsDNA binding motifs not only move to the most exterior surfaces, but also depart from the L1 and L2 ssDNA binding motifs.
[ "10", "29", "32", "28", "34", "3" ]
238
11,381
0
false
The strand exchange reaction between ssDNA and dsDNA likely occurs during this structural transition, since the HhH dsDNA binding motifs not only move to the most exterior surfaces, but also depart from the L1 and L2 ssDNA binding motifs.
[]
The strand exchange reaction between ssDNA and dsDNA likely occurs during this structural transition, since the HhH dsDNA binding motifs not only move to the most exterior surfaces, but also depart from the L1 and L2 ssDNA binding motifs.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Further, the two negatively charged residues of the E1–Ro–E2 triad are exposed to the filament surface and conceivably function to exclude ssDNA (Figure 6E).
[ "10", "29", "32", "28", "34", "3" ]
157
11,382
0
false
Further, the two negatively charged residues of the E1–Ro–E2 triad are exposed to the filament surface and conceivably function to exclude ssDNA (Figure 6E).
[]
Further, the two negatively charged residues of the E1–Ro–E2 triad are exposed to the filament surface and conceivably function to exclude ssDNA (Figure 6E).
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Finally, the left-handed filaments may dissociate from the heteroduplex DNA either via disassembly into RadA monomers or by carrying out a third ∼120° axial rotation to form P61 right-handed filaments.
[ "10", "29", "32", "28", "34", "3" ]
201
11,383
0
false
Finally, the left-handed filaments may dissociate from the heteroduplex DNA either via disassembly into RadA monomers or by carrying out a third ∼120° axial rotation to form P61 right-handed filaments.
[]
Finally, the left-handed filaments may dissociate from the heteroduplex DNA either via disassembly into RadA monomers or by carrying out a third ∼120° axial rotation to form P61 right-handed filaments.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Figure 10.Subunit rotation accounts for the structural transition of RecA right-handed filament from a compressed conformation (left panel) to a relaxed conformation (right panel).
[ "10", "29", "32", "28", "34", "3" ]
180
11,384
0
false
Figure 10.Subunit rotation accounts for the structural transition of RecA right-handed filament from a compressed conformation (left panel) to a relaxed conformation (right panel).
[]
Figure 10.Subunit rotation accounts for the structural transition of RecA right-handed filament from a compressed conformation (left panel) to a relaxed conformation (right panel).
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
The N-terminal domain (NTD, in gray), the polymerization motif (PM, in yellow), ATPase domain (in green) and C-terminal domain (in gray) are shown as indicated, respectively.
[ "10", "29", "32", "28", "34", "3" ]
174
11,385
0
false
The N-terminal domain (NTD, in gray), the polymerization motif (PM, in yellow), ATPase domain (in green) and C-terminal domain (in gray) are shown as indicated, respectively.
[]
The N-terminal domain (NTD, in gray), the polymerization motif (PM, in yellow), ATPase domain (in green) and C-terminal domain (in gray) are shown as indicated, respectively.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Ball-and-stick models of Ile27, Arg34 (R0), Glu19 are shown along with oxygen (red) and nitrogen (blue) atoms.
[ "10", "29", "32", "28", "34", "3" ]
110
11,386
0
false
Ball-and-stick models of Ile27, Arg34 (R0), Glu19 are shown along with oxygen (red) and nitrogen (blue) atoms.
[]
Ball-and-stick models of Ile27, Arg34, Glu19 are shown along with oxygen (red) and nitrogen (blue) atoms.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
The side chain of Ile27 (in yellow) is responsible for filament assembly via interacting with a hydrophobic site in the ATPase domain of neighboring promoter.
[ "10", "29", "32", "28", "34", "3" ]
158
11,387
0
false
The side chain of Ile27 (in yellow) is responsible for filament assembly via interacting with a hydrophobic site in the ATPase domain of neighboring promoter.
[]
The side chain of Ile27 (in yellow) is responsible for filament assembly via interacting with a hydrophobic site in the ATPase domain of neighboring promoter.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Arg34 forms a salt bridge with Glu19 in a compressed RecA helical filament (74 Å helical pitch, 33), and this salt bridge falls apart in a relaxed RecA helical filament (83 Γ… helical pitch, 29).
[ "10", "29", "32", "28", "34", "3" ]
194
11,388
0
false
Arg34 forms a salt bridge with Glu19 in a compressed RecA helical filament, and this salt bridge falls apart in a relaxed RecA helical filament.
[ "74 Å helical pitch, 33", "83 Γ… helical pitch, 29" ]
Arg34 forms a salt bridge with Glu19 in a compressed RecA helical filament, and this salt bridge falls apart in a relaxed RecA helical filament.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
The protein databank accession numbers of these two filaments are 1U94 and 2REB, respectively.
[ "10", "29", "32", "28", "34", "3" ]
94
11,389
0
false
The protein databank accession numbers of these two filaments are 1U94 and 2REB, respectively.
[]
The protein databank accession numbers of these two filaments are 1U94 and 2REB, respectively.
true
true
true
true
true
1,821
3
DISCUSSION
1
10
[ "B10", "B29", "B32", "B28", "B34", "B3" ]
17,329,376
pmid-15304222|pmid-15755748|pmid-11743724|pmid-11713300|pmid-15381077|pmid-15835894|pmid-16204247|pmid-15917244|pmid-11743724|pmid-11713300|pmid-15835894|pmid-16204247|pmid-15917244|pmid-15164066|pmid-15235592|pmid-1731246|pmid-16909421|pmid-16351198|pmid-8999937|pmid-14527291
Figure 11.The rotary motor hypothesis for RadA or Rad51 protein filaments.
[ "10", "29", "32", "28", "34", "3" ]
74
11,390
0
false
Figure 11.The rotary motor hypothesis for RadA or Rad51 protein filaments.
[]
Figure 11.The rotary motor hypothesis for RadA or Rad51 protein filaments.
true
true
true
true
true
1,821
4
DISCUSSION
0
null
null
17,329,376
null
Subunit rotation accounts for the structural transition of RecA right-handed filament from a compressed conformation (left panel) to a relaxed conformation (right panel).
null
170
11,391
0
false
null
null
Subunit rotation accounts for the structural transition of RecA right-handed filament from a compressed conformation (left panel) to a relaxed conformation (right panel).
true
true
true
true
true
1,822
4
DISCUSSION
0
null
null
17,329,376
null
The N-terminal domain (NTD, in gray), the polymerization motif (PM, in yellow), ATPase domain (in green) and C-terminal domain (in gray) are shown as indicated, respectively.
null
174
11,392
0
false
null
null
The N-terminal domain (NTD, in gray), the polymerization motif (PM, in yellow), ATPase domain (in green) and C-terminal domain (in gray) are shown as indicated, respectively.
true
true
true
true
true
1,822
4
DISCUSSION
0
null
null
17,329,376
null
Ball-and-stick models of Ile27, Arg34 (R0), Glu19 are shown along with oxygen (red) and nitrogen (blue) atoms.
null
110
11,393
0
false
null
null
Ball-and-stick models of Ile27, Arg34 (R0), Glu19 are shown along with oxygen (red) and nitrogen (blue) atoms.
true
true
true
true
true
1,822
4
DISCUSSION
0
null
null
17,329,376
null
The side chain of Ile27 (in yellow) is responsible for filament assembly via interacting with a hydrophobic site in the ATPase domain of neighboring promoter.
null
158
11,394
0
false
null
null
The side chain of Ile27 (in yellow) is responsible for filament assembly via interacting with a hydrophobic site in the ATPase domain of neighboring promoter.
true
true
true
true
true
1,822
4
DISCUSSION
0
null
null
17,329,376
null
Arg34 forms a salt bridge with Glu19 in a compressed RecA helical filament (74 Å helical pitch, 33), and this salt bridge falls apart in a relaxed RecA helical filament (83 Γ… helical pitch, 29).
null
194
11,395
0
false
null
null
Arg34 forms a salt bridge with Glu19 in a compressed RecA helical filament (74 Å helical pitch, 33), and this salt bridge falls apart in a relaxed RecA helical filament (83 Γ… helical pitch, 29).
true
true
true
true
true
1,822
4
DISCUSSION
0
null
null
17,329,376
null
The protein databank accession numbers of these two filaments are 1U94 and 2REB, respectively.
null
94
11,396
0
false
null
null
The protein databank accession numbers of these two filaments are 1U94 and 2REB, respectively.
true
true
true
true
true
1,822
5
DISCUSSION
0
null
null
17,329,376
null
The rotary motor hypothesis for RadA or Rad51 protein filaments.
null
64
11,397
0
false
null
null
The rotary motor hypothesis for RadA or Rad51 protein filaments.
true
true
true
true
true
1,823
6
DISCUSSION
1
35
[ "B35", "B36", "B37" ]
17,329,376
pmid-2067019|pmid-2067020|pmid-11268201
Subunit rotation may also occur in other helical protein filaments.
[ "35", "36", "37" ]
67
11,398
0
false
Subunit rotation may also occur in other helical protein filaments.
[]
Subunit rotation may also occur in other helical protein filaments.
true
true
true
true
true
1,824
6
DISCUSSION
1
35
[ "B35", "B36", "B37" ]
17,329,376
pmid-2067019|pmid-2067020|pmid-11268201
For example, it has been shown that subunit rotation controls the right-handed to left-handed transition of the Salmonella typhimurium flagellar filament (35).
[ "35", "36", "37" ]
159
11,399
1
false
For example, it has been shown that subunit rotation controls the right-handed to left-handed transition of the Salmonella typhimurium flagellar filament.
[ "35" ]
For example, it has been shown that subunit rotation controls the right-handed to left-handed transition of the Salmonella typhimurium flagellar filament.
true
true
true
true
true
1,824