Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
1
DISCUSSION
1
10
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For a complete analysis of all models please see reference (10).
[ "18", "10", "23–33", "10" ]
64
1,100
1
false
For a complete analysis of all models please see reference.
[ "10" ]
For a complete analysis of all models please see reference.
true
true
true
true
true
190
2
DISCUSSION
1
23–33
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
Examples of ‘FastContact’ scoring for a subset of high quality docked models from eight groups for targets 8 and 12 of CAPRI rounds 3–5, from http://capri.ebi.ac.uk/.
[ "23–33", "10" ]
166
1,101
0
false
Examples of ‘FastContact’ scoring for a subset of high quality docked models from eight groups for targets 8 and 12 of CAPRI rounds 3–5, from http://capri.ebi.ac.uk/.
[]
Examples of ‘FastContact’ scoring for a subset of high quality docked models from eight groups for targets 8 and 12 of CAPRI rounds 3–5, from http://capri.ebi.ac.uk/.
true
true
true
true
true
191
2
DISCUSSION
1
23–33
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For each of these targets, we run the models in our server and re-rank the models accordingly.
[ "23–33", "10" ]
94
1,102
0
false
For each of these targets, we run the models in our server and re-rank the models accordingly.
[]
For each of these targets, we run the models in our server and re-rank the models accordingly.
true
true
true
true
true
191
2
DISCUSSION
1
23–33
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
In all cases, the server was able to correctly rank a low RMSD model as the one with the lowest free energy score.
[ "23–33", "10" ]
114
1,103
0
false
In all cases, the server was able to correctly rank a low RMSD model as the one with the lowest free energy score.
[]
In all cases, the server was able to correctly rank a low RMSD model as the one with the lowest free energy score.
true
true
true
true
true
191
2
DISCUSSION
1
23–33
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For comparison, we also marked with a diamond symbol the model ranked number 1 by the modeler (23–33).
[ "23–33", "10" ]
102
1,104
1
false
For comparison, we also marked with a diamond symbol the model ranked number 1 by the modeler.
[ "23–33" ]
For comparison, we also marked with a diamond symbol the model ranked number 1 by the modeler.
true
true
true
true
true
191
2
DISCUSSION
1
23–33
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
(A) target 8; (B) target 12.
[ "23–33", "10" ]
28
1,105
0
false
(A) target 8; (B) target 12.
[]
(A) target 8; (B) target 12.
false
false
true
true
false
191
2
DISCUSSION
1
10
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For a complete analysis of all models please see reference (10).
[ "23–33", "10" ]
64
1,106
1
false
For a complete analysis of all models please see reference.
[ "10" ]
For a complete analysis of all models please see reference.
true
true
true
true
true
191
3
DISCUSSION
1
21
[ "B21", "B22" ]
17,537,824
pmid-10049302|pmid-14693807
By splitting the free energy between electrostatics and desolvation, ‘Fastcontact’ also provides immediate insights into the nature of the binding interactions.
[ "21", "22" ]
160
1,107
0
false
By splitting the free energy between electrostatics and desolvation, ‘Fastcontact’ also provides immediate insights into the nature of the binding interactions.
[]
By splitting the free energy between electrostatics and desolvation, ‘Fastcontact’ also provides immediate insights into the nature of the binding interactions.
true
true
true
true
true
192
3
DISCUSSION
1
21
[ "B21", "B22" ]
17,537,824
pmid-10049302|pmid-14693807
Namely, negative desolvation is associated with a hydrophobic pocket at the binding site, whereas positive desolvation characterizes mostly polar interfaces.
[ "21", "22" ]
157
1,108
0
false
Namely, negative desolvation is associated with a hydrophobic pocket at the binding site, whereas positive desolvation characterizes mostly polar interfaces.
[]
Namely, negative desolvation is associated with a hydrophobic pocket at the binding site, whereas positive desolvation characterizes mostly polar interfaces.
true
true
true
true
true
192
3
DISCUSSION
1
21
[ "B21", "B22" ]
17,537,824
pmid-10049302|pmid-14693807
This is important since sometimes electrostatic or desolvation alone could lead to better discrimination than the combination of the two (21,22).
[ "21", "22" ]
145
1,109
0
false
This is important since sometimes electrostatic or desolvation alone could lead to better discrimination than the combination of the two.
[ "21,22" ]
This is important since sometimes electrostatic or desolvation alone could lead to better discrimination than the combination of the two.
true
true
true
true
true
192
3
DISCUSSION
1
21
[ "B21", "B22" ]
17,537,824
pmid-10049302|pmid-14693807
The latter is, of course, due to the intrinsic limitations of empirical free energies.
[ "21", "22" ]
86
1,110
0
false
The latter is, of course, due to the intrinsic limitations of empirical free energies.
[]
The latter is, of course, due to the intrinsic limitations of empirical free energies.
true
true
true
true
true
192
3
DISCUSSION
1
21
[ "B21", "B22" ]
17,537,824
pmid-10049302|pmid-14693807
In particular, reliable estimates for solvent and entropic interactions are not yet available.
[ "21", "22" ]
94
1,111
0
false
In particular, reliable estimates for solvent and entropic interactions are not yet available.
[]
In particular, reliable estimates for solvent and entropic interactions are not yet available.
true
true
true
true
true
192
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b8" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
Colicins, which are produced by bacteria carrying the corresponding Col plasmids, kill sensitive Escherichia coli cells through activities involving the ion channels in the inner membranes, DNases or RNases (1,2).
[ "1", "2", "3", "5", "6", "8" ]
213
1,112
0
false
Colicins, which are produced by bacteria carrying the corresponding Col plasmids, kill sensitive Escherichia coli cells through activities involving the ion channels in the inner membranes, DNases or RNases.
[ "1,2" ]
Colicins, which are produced by bacteria carrying the corresponding Col plasmids, kill sensitive Escherichia coli cells through activities involving the ion channels in the inner membranes, DNases or RNases.
true
true
true
true
true
193
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b8" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
The DNase-type colicins nonspecifically degrade the genomic DNAs of the sensitive cells (3–5), whereas those of the RNase type cleave 16S rRNA at the 49th phosphodiester bond from the 3′ end (6–8).
[ "1", "2", "3", "5", "6", "8" ]
197
1,113
0
false
The DNase-type colicins nonspecifically degrade the genomic DNAs of the sensitive cells, whereas those of the RNase type cleave 16S rRNA at the 49th phosphodiester bond from the 3′ end.
[ "3–5", "6–8" ]
The DNase-type colicins nonspecifically degrade the genomic DNAs of the sensitive cells, whereas those of the RNase type cleave 16S rRNA at the 49th phosphodiester bond from the 3′ end.
true
true
true
true
true
193
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b8" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
These colicins contain three domains—a membrane-translocating domain, a receptor-binding domain, and a catalytic domain—in their primary sequences.
[ "1", "2", "3", "5", "6", "8" ]
147
1,114
0
false
These colicins contain three domains—a membrane-translocating domain, a receptor-binding domain, and a catalytic domain—in their primary sequences.
[]
These colicins contain three domains—a membrane-translocating domain, a receptor-binding domain, and a catalytic domain—in their primary sequences.
true
true
true
true
true
193
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b8" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
Colicinogenic cells also produce inhibitor proteins (Imm), the genes for which are located downstream of the col genes in the colicin operons that are under the control of the SOS-dependent promoters.
[ "1", "2", "3", "5", "6", "8" ]
200
1,115
0
false
Colicinogenic cells also produce inhibitor proteins (Imm), the genes for which are located downstream of the col genes in the colicin operons that are under the control of the SOS-dependent promoters.
[]
Colicinogenic cells also produce inhibitor proteins (Imm), the genes for which are located downstream of the col genes in the colicin operons that are under the control of the SOS-dependent promoters.
true
true
true
true
true
193
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b8" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
Imms bind specifically to cognate colicins in order to protect their host cells.
[ "1", "2", "3", "5", "6", "8" ]
80
1,116
0
false
Imms bind specifically to cognate colicins in order to protect their host cells.
[]
Imms bind specifically to cognate colicins in order to protect their host cells.
true
true
true
true
true
193
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
In addition to the known RNase-type colicins, colicin E5 that has been recently characterized as a tRNase has a unique target for its toxicity.
[ "9", "10", "11", "12" ]
143
1,117
0
false
In addition to the known RNase-type colicins, colicin E5 that has been recently characterized as a tRNase has a unique target for its toxicity.
[]
In addition to the known RNase-type colicins, colicin E5 that has been recently characterized as a tRNase has a unique target for its toxicity.
true
true
true
true
true
194
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
It specifically cleaves the anticodons of E.coli tRNAs for Tyr, His, Asn and Asp.
[ "9", "10", "11", "12" ]
81
1,118
0
false
It specifically cleaves the anticodons of E.coli tRNAs for Tyr, His, Asn and Asp.
[]
It specifically cleaves the anticodons of E.coli tRNAs for Tyr, His, Asn and Asp.
true
true
true
true
true
194
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
These tRNAs decode NAY (N: any nucleotide, A: adenosine and Y: a pyrimidine nucleotide) codons by means of QUN anticodons, where queuosine (Q) is a 7-deazaguanosine with a cyclopentenediol side chain (9).
[ "9", "10", "11", "12" ]
204
1,119
1
false
These tRNAs decode NAY (N: any nucleotide, A: adenosine and Y: a pyrimidine nucleotide) codons by means of QUN anticodons, where queuosine (Q) is a 7-deazaguanosine with a cyclopentenediol side chain.
[ "9" ]
These tRNAs decode NAY (N: any nucleotide, A: adenosine and Y: a pyrimidine nucleotide) codons by means of QUN anticodons, where queuosine (Q) is a 7-deazaguanosine with a cyclopentenediol side chain.
true
true
true
true
true
194
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
Initially, colicin E5 was observed to cleave only the QU sequence of these tRNAs between positions 34 and 35, leaving a 2′,3′-cyclic phosphate on Q and a 5′-OH on U.
[ "9", "10", "11", "12" ]
165
1,120
0
false
Initially, colicin E5 was observed to cleave only the QU sequence of these tRNAs between positions 34 and 35, leaving a 2′,3′-cyclic phosphate on Q and a 5′-OH on U.
[]
Initially, colicin E5 was observed to cleave only the QU sequence of these tRNAs between positions 34 and 35, leaving a 2′,3′-cyclic phosphate on Q and a 5′-OH on U.
true
true
true
true
true
194
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
In tRNA-guanine transglycosylase-deficient strains the inherent G is not replaced with a precursor base of Q; this gives rise to tRNAs with GUN anticodons.
[ "9", "10", "11", "12" ]
155
1,121
0
false
In tRNA-guanine transglycosylase-deficient strains the inherent G is not replaced with a precursor base of Q; this gives rise to tRNAs with GUN anticodons.
[]
In tRNA-guanine transglycosylase-deficient strains the inherent G is not replaced with a precursor base of Q; this gives rise to tRNAs with GUN anticodons.
true
true
true
true
true
194
1
INTRODUCTION
1
10
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
These strains were demonstrated to be sensitive to colicin E5; the tRNAs were still subjected to cleavage (10).
[ "9", "10", "11", "12" ]
111
1,122
1
false
These strains were demonstrated to be sensitive to colicin E5; the tRNAs were still subjected to cleavage.
[ "10" ]
These strains were demonstrated to be sensitive to colicin E5; the tRNAs were still subjected to cleavage.
true
true
true
true
true
194
1
INTRODUCTION
1
11
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
It is assumed that colicin E5 consists of 556 amino acids (11).
[ "9", "10", "11", "12" ]
63
1,123
1
false
It is assumed that colicin E5 consists of 556 amino acids.
[ "11" ]
It is assumed that colicin E5 consists of 556 amino acids.
true
true
true
true
true
194
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
The ribonuclease activity of E5 resides solely within its C-terminal ribonuclease domain (E5-CRD; 115 amino acids), and this domain is responsible for its substrate specificity.
[ "9", "10", "11", "12" ]
177
1,124
0
false
The ribonuclease activity of E5 resides solely within its C-terminal ribonuclease domain, and this domain is responsible for its substrate specificity.
[ "E5-CRD; 115 amino acids" ]
The ribonuclease activity of E5 resides solely within its C-terminal ribonuclease domain, and this domain is responsible for its substrate specificity.
true
true
true
true
true
194
1
INTRODUCTION
1
12
[ "b9", "b10", "b11", "b12" ]
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
Furthermore, based on the results obtained from our assay using synthetic minihelices or linear oligoribonucleotides, E5-CRD can be referred to as an RNA restriction enzyme that specifically recognizes and cleaves single-stranded GU sequences (12).
[ "9", "10", "11", "12" ]
248
1,125
1
false
Furthermore, based on the results obtained from our assay using synthetic minihelices or linear oligoribonucleotides, E5-CRD can be referred to as an RNA restriction enzyme that specifically recognizes and cleaves single-stranded GU sequences.
[ "12" ]
Furthermore, based on the results obtained from our assay using synthetic minihelices or linear oligoribonucleotides, E5-CRD can be referred to as an RNA restriction enzyme that specifically recognizes and cleaves single-stranded GU sequences.
true
true
true
true
true
194
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
In addition to colicin E5, colicin D (13), PrrC (14) and zymocin (15) are also known to be tRNases.
[ "13", "14", "15", "16", "17" ]
99
1,126
1
false
In addition to colicin E5, colicin D, PrrC and zymocin are also known to be tRNases.
[ "13", "14", "15" ]
In addition to colicin E5, colicin D, PrrC and zymocin are also known to be tRNases.
true
true
true
true
true
195
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
However, these enzymes are nonhomologous with each other and target tRNAs and cleavage sites that are different from those targeted by colicin E5.
[ "13", "14", "15", "16", "17" ]
146
1,127
0
false
However, these enzymes are nonhomologous with each other and target tRNAs and cleavage sites that are different from those targeted by colicin E5.
[]
However, these enzymes are nonhomologous with each other and target tRNAs and cleavage sites that are different from those targeted by colicin E5.
true
true
true
true
true
195
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
Colicin D, which is produced by E.coli harboring a ColD plasmid, cleaves only four isoacceptors of tRNAArg between positions 38 and 39 at the 3′ junction of the anticodon stem and loop.
[ "13", "14", "15", "16", "17" ]
185
1,128
0
false
Colicin D, which is produced by E.coli harboring a ColD plasmid, cleaves only four isoacceptors of tRNAArg between positions 38 and 39 at the 3′ junction of the anticodon stem and loop.
[]
Colicin D, which is produced by E.coli harboring a ColD plasmid, cleaves only four isoacceptors of tRNAArg between positions 38 and 39 at the 3′ junction of the anticodon stem and loop.
true
true
true
true
true
195
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
PrrC is induced in some E.coli isolates by T4 phage infection, and it only cleaves tRNALys between positions 33 and 34 at the 5′ side of the anticodon.
[ "13", "14", "15", "16", "17" ]
151
1,129
0
false
PrrC is induced in some E.coli isolates by T4 phage infection, and it only cleaves tRNALys between positions 33 and 34 at the 5′ side of the anticodon.
[]
PrrC is induced in some E.coli isolates by T4 phage infection, and it only cleaves tRNALys between positions 33 and 34 at the 5′ side of the anticodon.
true
true
true
true
true
195
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
Zymocin, which is produced by Kluyveromyces lactis, was recently reported to cleave some yeast tRNAs at the 3′ side of the modified nucleotide U in the anticodons of 5-methoxycarbonylmethyl-2-thiouridine uridine cytosine (mcm5s2UUC), mcm5s2UUU
[ "13", "14", "15", "16", "17" ]
243
1,130
0
false
Zymocin, which is produced by Kluyveromyces lactis, was recently reported to cleave some yeast tRNAs at the 3′ side of the modified nucleotide U in the anticodons of 5-methoxycarbonylmethyl-2-thiouridine uridine cytosine (mcm5s2UUC), mcm5s2UUU
[]
Zymocin, which is produced by Kluyveromyces lactis, was recently reported to cleave some yeast tRNAs at the 3′ side of the modified nucleotide U in the anticodons of 5-methoxycarbonylmethyl-2-thiouridine uridine cytosine (mcm5s2UUC), mcm5s2UUU
true
true
false
true
false
195
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
and mcm5s2UUG.
[ "13", "14", "15", "16", "17" ]
14
1,131
0
false
and mcm5s2UUG.
[]
and mcm5s2UUG.
false
true
true
true
false
195
2
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17" ]
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
Among these tRNases, the crystal structure of the C-terminal catalytic domain of colicin D (D-CRD) has been solved (16,17); the structure revealed a curved row of basic residues on the molecular surface that could confer the tRNA recognition specificity.
[ "13", "14", "15", "16", "17" ]
254
1,132
0
false
Among these tRNases, the crystal structure of the C-terminal catalytic domain of colicin D (D-CRD) has been solved ; the structure revealed a curved row of basic residues on the molecular surface that could confer the tRNA recognition specificity.
[ "16,17" ]
Among these tRNases, the crystal structure of the C-terminal catalytic domain of colicin D (D-CRD) has been solved ; the structure revealed a curved row of basic residues on the molecular surface that could confer the tRNA recognition specificity.
true
true
true
true
true
195
3
INTRODUCTION
1
18
[ "b18", "b19" ]
17,099,236
pmid-15537630|pmid-12526800
ImmE5—a specific inhibitor protein of colicin E5—is expressed in host cells and binds to E5-CRD to prevent cell death.
[ "18", "19" ]
118
1,133
0
false
ImmE5—a specific inhibitor protein of colicin E5—is expressed in host cells and binds to E5-CRD to prevent cell death.
[]
ImmE5—a specific inhibitor protein of colicin E5—is expressed in host cells and binds to E5-CRD to prevent cell death.
true
true
true
true
true
196
3
INTRODUCTION
1
18
[ "b18", "b19" ]
17,099,236
pmid-15537630|pmid-12526800
In addition to the nuclease-type colicin family, this type of proteinaceous toxin–antitoxin system (comprising addiction molecules), including MazE/F (18) and RelB/E (19) whose targets are considered to be the ACA sequences in mRNAs and stop codons of mRNAs in the ribosomal A site, respectively, has also been well studied.
[ "18", "19" ]
324
1,134
1
false
In addition to the nuclease-type colicin family, this type of proteinaceous toxin–antitoxin system (comprising addiction molecules), including MazE/F and RelB/E whose targets are considered to be the ACA sequences in mRNAs and stop codons of mRNAs in the ribosomal A site, respectively, has also been well studied.
[ "18", "19" ]
In addition to the nuclease-type colicin family, this type of proteinaceous toxin–antitoxin system (comprising addiction molecules), including MazE/F and RelB/E whose targets are considered to be the ACA sequences in mRNAs and stop codons of mRNAs in the ribosomal A site, respectively, has also been well studied.
true
true
true
true
true
196
3
INTRODUCTION
1
18
[ "b18", "b19" ]
17,099,236
pmid-15537630|pmid-12526800
The study of these molecules reveals the survival mechanism in bacteria; additionally, they serve as very good examples of protein–protein interactions.
[ "18", "19" ]
152
1,135
0
false
The study of these molecules reveals the survival mechanism in bacteria; additionally, they serve as very good examples of protein–protein interactions.
[]
The study of these molecules reveals the survival mechanism in bacteria; additionally, they serve as very good examples of protein–protein interactions.
true
true
true
true
true
196
3
INTRODUCTION
1
18
[ "b18", "b19" ]
17,099,236
pmid-15537630|pmid-12526800
Furthermore, from the structural viewpoint, it is of special interest to determine whether ribonuclease inhibitors, i.e.
[ "18", "19" ]
120
1,136
0
false
Furthermore, from the structural viewpoint, it is of special interest to determine whether ribonuclease inhibitors, i.e.
[]
Furthermore, from the structural viewpoint, it is of special interest to determine whether ribonuclease inhibitors, i.e.
true
true
true
true
true
196
3
INTRODUCTION
1
18
[ "b18", "b19" ]
17,099,236
pmid-15537630|pmid-12526800
inhibitors of toxins that target DNA or RNA, bind to the corresponding enzymes by mimicking the substrate RNAs/DNAs.
[ "18", "19" ]
116
1,137
0
false
inhibitors of toxins that target DNA or RNA, bind to the corresponding enzymes by mimicking the substrate RNAs/DNAs.
[]
inhibitors of toxins that target DNA or RNA, bind to the corresponding enzymes by mimicking the substrate RNAs/DNAs.
false
true
true
true
false
196
4
INTRODUCTION
0
null
null
17,099,236
pmid-14580342|pmid-15901733|pmid-12718874
Further, although E5-CRD exhibits ribonuclease activity, it lacks His that usually serves as a catalytic residue in all known ribonucleases.
null
140
1,138
0
false
null
null
Further, although E5-CRD exhibits ribonuclease activity, it lacks His that usually serves as a catalytic residue in all known ribonucleases.
true
true
true
true
true
197
4
INTRODUCTION
0
null
null
17,099,236
pmid-14580342|pmid-15901733|pmid-12718874
Thus, E5-CRD must have an alternative mechanism that is responsible for its ribonuclease activity.
null
98
1,139
0
false
null
null
Thus, E5-CRD must have an alternative mechanism that is responsible for its ribonuclease activity.
true
true
true
true
true
197
5
INTRODUCTION
1
20
[ "b20", "b21" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Since E5-CRD shows no homology with any other proteins, we performed the structural analysis of E5-CRD in order to explore the novel features of colicin E5.
[ "20", "21" ]
156
1,140
0
false
Since E5-CRD shows no homology with any other proteins, we performed the structural analysis of E5-CRD in order to explore the novel features of colicin E5.
[]
Since E5-CRD shows no homology with any other proteins, we performed the structural analysis of E5-CRD in order to explore the novel features of colicin E5.
true
true
true
true
true
198
5
INTRODUCTION
1
20
[ "b20", "b21" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Recently, Huang's group has reported the structures of E5-CRD (20) and E5-CRD complexed with ImmE5 (21) at a resolution of 1.5 and 1.15 Å, respectively; they also proposed a putative model of the interaction between E5-CRD and tRNA.
[ "20", "21" ]
232
1,141
1
false
Recently, Huang's group has reported the structures of E5-CRD and E5-CRD complexed with ImmE5 at a resolution of 1.5 and 1.15 Å, respectively; they also proposed a putative model of the interaction between E5-CRD and tRNA.
[ "20", "21" ]
Recently, Huang's group has reported the structures of E5-CRD and E5-CRD complexed with ImmE5 at a resolution of 1.5 and 1.15 Å, respectively; they also proposed a putative model of the interaction between E5-CRD and tRNA.
true
true
true
true
true
198
5
INTRODUCTION
1
20
[ "b20", "b21" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
However, the precise structure of the active site in the pocket with catalytic residues remains unknown.
[ "20", "21" ]
104
1,142
0
false
However, the precise structure of the active site in the pocket with catalytic residues remains unknown.
[]
However, the precise structure of the active site in the pocket with catalytic residues remains unknown.
true
true
true
true
true
198
5
INTRODUCTION
1
20
[ "b20", "b21" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Here, we report the crystal structures of E5-CRD complexed with its substrate analog and E5-CRD complexed with ImmE5.
[ "20", "21" ]
117
1,143
0
false
Here, we report the crystal structures of E5-CRD complexed with its substrate analog and E5-CRD complexed with ImmE5.
[]
Here, we report the crystal structures of E5-CRD complexed with its substrate analog and E5-CRD complexed with ImmE5.
true
true
true
true
true
198
5
INTRODUCTION
1
20
[ "b20", "b21" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
These structures clearly demonstrate the mechanism by which specific substrate recognition is achieved and reveal the residues that could play important roles for the catalytic activity in the absence of His.
[ "20", "21" ]
208
1,144
0
false
These structures clearly demonstrate the mechanism by which specific substrate recognition is achieved and reveal the residues that could play important roles for the catalytic activity in the absence of His.
[]
These structures clearly demonstrate the mechanism by which specific substrate recognition is achieved and reveal the residues that could play important roles for the catalytic activity in the absence of His.
true
true
true
true
true
198
5
INTRODUCTION
1
20
[ "b20", "b21" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Based on these structures, we propose the double mimicry model to demonstrate the mechanism by which the protein–protein interaction replaces the RNA–RNA interaction.
[ "20", "21" ]
166
1,145
0
false
Based on these structures, we propose the double mimicry model to demonstrate the mechanism by which the protein–protein interaction replaces the RNA–RNA interaction.
[]
Based on these structures, we propose the double mimicry model to demonstrate the mechanism by which the protein–protein interaction replaces the RNA–RNA interaction.
true
true
true
true
true
198
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
Among the colicin family proteins, the crystal structure of RNase-type colicin E3 has been reported (27,28).
[ "27", "28" ]
108
1,146
0
false
Among the colicin family proteins, the crystal structure of RNase-type colicin E3 has been reported.
[ "27,28" ]
Among the colicin family proteins, the crystal structure of RNase-type colicin E3 has been reported.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
Colicins E3 and E5 are homologous at the receptor-binding and membrane-translocating domains.
[ "27", "28" ]
93
1,147
0
false
Colicins E3 and E5 are homologous at the receptor-binding and membrane-translocating domains.
[]
Colicins E3 and E5 are homologous at the receptor-binding and membrane-translocating domains.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
On the other hand, the catalytic domains of both these colicins showed no homology, reflecting completely different targets.
[ "27", "28" ]
124
1,148
0
false
On the other hand, the catalytic domains of both these colicins showed no homology, reflecting completely different targets.
[]
On the other hand, the catalytic domains of both these colicins showed no homology, reflecting completely different targets.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
Colicin E5 is a tRNase that specifically targets the GU and QU sequences of the anticodons specifically.
[ "27", "28" ]
104
1,149
0
false
Colicin E5 is a tRNase that specifically targets the GU and QU sequences of the anticodons specifically.
[]
Colicin E5 is a tRNase that specifically targets the GU and QU sequences of the anticodons specifically.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
In order to understand this specific recognition mechanism, we solved the crystal structure of the C-terminal tRNase domain of colicin E5 complexed with its substrate analog, dGpdUp.
[ "27", "28" ]
182
1,150
0
false
In order to understand this specific recognition mechanism, we solved the crystal structure of the C-terminal tRNase domain of colicin E5 complexed with its substrate analog, dGpdUp.
[]
In order to understand this specific recognition mechanism, we solved the crystal structure of the C-terminal tRNase domain of colicin E5 complexed with its substrate analog, dGpdUp.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
The tight binding of dGpdUp to E5-CRD was achieved by ring–ring-interactions and the maximum possible hydrogen bonds, suggesting the mimicry of Watson–Crick-type interactions in both dG and dU (Figure 3A and C).
[ "27", "28" ]
211
1,151
0
false
The tight binding of dGpdUp to E5-CRD was achieved by ring–ring-interactions and the maximum possible hydrogen bonds, suggesting the mimicry of Watson–Crick-type interactions in both dG and dU (Figure 3A and C).
[]
The tight binding of dGpdUp to E5-CRD was achieved by ring–ring-interactions and the maximum possible hydrogen bonds, suggesting the mimicry of Watson–Crick-type interactions in both dG and dU (Figure 3A and C).
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
If the dG base were to be substituted by dA, none of these hydrogen bonds would be possible.
[ "27", "28" ]
92
1,152
0
false
If the dG base were to be substituted by dA, none of these hydrogen bonds would be possible.
[]
If the dG base were to be substituted by dA, none of these hydrogen bonds would be possible.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
In contrast, if the same dG base was to be substituted by a Q base, all these hydrogen bonds would be retained, while the modification extending from the N7 position would easily extend into the solvent.
[ "27", "28" ]
203
1,153
0
false
In contrast, if the same dG base was to be substituted by a Q base, all these hydrogen bonds would be retained, while the modification extending from the N7 position would easily extend into the solvent.
[]
In contrast, if the same dG base was to be substituted by a Q base, all these hydrogen bonds would be retained, while the modification extending from the N7 position would easily extend into the solvent.
true
true
true
true
true
199
0
DISCUSSION
1
27
[ "b27", "b28" ]
17,099,236
pmid-8757721|pmid-12423780|pmid-1069283|pmid-9716496|pmid-4930244|pmid-4930243|pmid-10986462|pmid-11741540
The above modeling consideration is consistent with the experimental observation that the tRNAs with Q as well as the corresponding molecules without Q are cleaved by E5-CRD.
[ "27", "28" ]
174
1,154
0
false
The above modeling consideration is consistent with the experimental observation that the tRNAs with Q as well as the corresponding molecules without Q are cleaved by E5-CRD.
[]
The above modeling consideration is consistent with the experimental observation that the tRNAs with Q as well as the corresponding molecules without Q are cleaved by E5-CRD.
true
true
true
true
true
199
1
DISCUSSION
0
null
null
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
If the dU base were to be substituted by dC, only one hydrogen bond would be retained.
null
86
1,155
0
false
null
null
If the dU base were to be substituted by dC, only one hydrogen bond would be retained.
true
true
true
true
true
200
1
DISCUSSION
0
null
null
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
Thus, the nucleotide sequence G (or Q)-U appears to be favored by E5-CRD through the formation of maximum possible hydrogen bonds and aromatic ring (or pseudo ring) stacking interactions.
null
187
1,156
0
false
null
null
Thus, the nucleotide sequence G (or Q)-U appears to be favored by E5-CRD through the formation of maximum possible hydrogen bonds and aromatic ring (or pseudo ring) stacking interactions.
true
true
true
true
true
200
1
DISCUSSION
0
null
null
17,099,236
pmid-388227|pmid-10092236|pmid-2549375|NA
All the hydrogen bonds use the backbone amide N or carbonyl O of E5-CRD, except hydroxyl O of Ser52.
null
100
1,157
0
false
null
null
All the hydrogen bonds use the backbone amide N or carbonyl O of E5-CRD, except hydroxyl O of Ser52.
true
true
true
true
true
200
2
DISCUSSION
0
null
null
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
In addition to the interactions of the bases by the hydrogen bonds and ring interactions, backbone phosphates are also retained by several hydrogen bonds.
null
154
1,158
0
false
null
null
In addition to the interactions of the bases by the hydrogen bonds and ring interactions, backbone phosphates are also retained by several hydrogen bonds.
true
true
true
true
true
201
2
DISCUSSION
0
null
null
17,099,236
pmid-10880568|pmid-10664586|pmid-16244131|pmid-15014439|pmid-15336558
Thus, this observation also suggests that E5-CRD has less flexibility for substrate recognition; this results in binding to only the specific target.
null
149
1,159
0
false
null
null
Thus, this observation also suggests that E5-CRD has less flexibility for substrate recognition; this results in binding to only the specific target.
true
true
true
true
true
201
3
DISCUSSION
0
null
null
17,099,236
pmid-15537630|pmid-12526800
These findings explain that the specific cleavage of the Q(G)UN anticodon sequence by E5-CRD is based on the GU-specific base recognition by E5-CRD.
null
148
1,160
0
false
null
null
These findings explain that the specific cleavage of the Q(G)UN anticodon sequence by E5-CRD is based on the GU-specific base recognition by E5-CRD.
true
true
true
true
true
202
3
DISCUSSION
0
null
null
17,099,236
pmid-15537630|pmid-12526800
In addition, this specific recognition between the protein and the RNA is realized in a manner similar to the Watson–Crick-type interaction used in an RNA double strand.
null
169
1,161
0
false
null
null
In addition, this specific recognition between the protein and the RNA is realized in a manner similar to the Watson–Crick-type interaction used in an RNA double strand.
true
true
true
true
true
202
4
DISCUSSION
1
29
[ "b29", "b30", "b31" ]
17,099,236
pmid-14580342|pmid-15901733|pmid-12718874
There are several examples of RNAs being processed in a site-specific manner.
[ "29", "30", "31" ]
77
1,162
0
false
There are several examples of RNAs being processed in a site-specific manner.
[]
There are several examples of RNAs being processed in a site-specific manner.
true
true
true
true
true
203
4
DISCUSSION
1
29
[ "b29", "b30", "b31" ]
17,099,236
pmid-14580342|pmid-15901733|pmid-12718874
MazF and ChpBK cleave free RNAs at the ACA and ACY (Y: U, A or G) sequences, respectively (29,30).
[ "29", "30", "31" ]
98
1,163
0
false
MazF and ChpBK cleave free RNAs at the ACA and ACY (Y: U, A or G) sequences, respectively.
[ "29,30" ]
MazF and ChpBK cleave free RNAs at the ACA and ACY (Y: U, A or G) sequences, respectively.
true
true
true
true
true
203
4
DISCUSSION
1
29
[ "b29", "b30", "b31" ]
17,099,236
pmid-14580342|pmid-15901733|pmid-12718874
Both proteins are E.coli chromosomal toxins and inhibit translation by cleaving mRNA.
[ "29", "30", "31" ]
85
1,164
0
false
Both proteins are E.coli chromosomal toxins and inhibit translation by cleaving mRNA.
[]
Both proteins are E.coli chromosomal toxins and inhibit translation by cleaving mRNA.
true
true
true
true
true
203
4
DISCUSSION
1
31
[ "b29", "b30", "b31" ]
17,099,236
pmid-14580342|pmid-15901733|pmid-12718874
The crystal structure of MazF has been recently reported (31); however, no structural information on its substrate binding is available.
[ "29", "30", "31" ]
136
1,165
1
false
The crystal structure of MazF has been recently reported ; however, no structural information on its substrate binding is available.
[ "31" ]
The crystal structure of MazF has been recently reported ; however, no structural information on its substrate binding is available.
true
true
true
true
true
203
5
DISCUSSION
1
10
[ "b10" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Although there should be a large number of GU sequences in cellular RNAs, E5 preferentially acts on tRNA anticodons in vivo (10).
[ "10" ]
129
1,166
1
false
Although there should be a large number of GU sequences in cellular RNAs, E5 preferentially acts on tRNA anticodons in vivo.
[ "10" ]
Although there should be a large number of GU sequences in cellular RNAs, E5 preferentially acts on tRNA anticodons in vivo.
true
true
true
true
true
204
5
DISCUSSION
1
10
[ "b10" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
When we docked E5-CRD and a tRNA molecule (tRNAAsp, PDB code 1ASY) manually by superimposing dGpdUp and GU of the tRNA, E5-CRD made contact only with the anticodon arm of tRNA (Figure 5).
[ "10" ]
187
1,167
0
false
When we docked E5-CRD and a tRNA molecule (tRNAAsp, PDB code 1ASY) manually by superimposing dGpdUp and GU of the tRNA, E5-CRD made contact only with the anticodon arm of tRNA (Figure 5).
[]
When we docked E5-CRD and a tRNA molecule manually by superimposing dGpdUp and GU of the tRNA, E5-CRD made contact only with the anticodon arm of tRNA (Figure 5).
true
true
true
true
true
204
5
DISCUSSION
1
10
[ "b10" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Interestingly, the parallel helix of E5-CRD fits in the helix of the anticodon arm.
[ "10" ]
83
1,168
0
false
Interestingly, the parallel helix of E5-CRD fits in the helix of the anticodon arm.
[]
Interestingly, the parallel helix of E5-CRD fits in the helix of the anticodon arm.
true
true
true
true
true
204
5
DISCUSSION
1
10
[ "b10" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
This may explain the substrate specificity of tRNA, where E5-CRD tightly binds to tRNA thereby allowing the capture of G–U bases at the bottom of the binding pocket.
[ "10" ]
165
1,169
0
false
This may explain the substrate specificity of tRNA, where E5-CRD tightly binds to tRNA thereby allowing the capture of G–U bases at the bottom of the binding pocket.
[]
This may explain the substrate specificity of tRNA, where E5-CRD tightly binds to tRNA thereby allowing the capture of G–U bases at the bottom of the binding pocket.
true
true
true
true
true
204
5
DISCUSSION
1
10
[ "b10" ]
17,099,236
pmid-16060658|pmid-16524591|pmid-10092236
Therefore, E5-CRD may prefer GU sequences embedded in specific secondary structures such as anticodon loops, and in fact, the enzyme kinetic study also demonstrated this GU preference by E5-CRD (12).
[ "10" ]
199
1,170
0
false
Therefore, E5-CRD may prefer GU sequences embedded in specific secondary structures such as anticodon loops, and in fact, the enzyme kinetic study also demonstrated this GU preference by E5-CRD (12).
[]
Therefore, E5-CRD may prefer GU sequences embedded in specific secondary structures such as anticodon loops, and in fact, the enzyme kinetic study also demonstrated this GU preference by E5-CRD.
true
true
true
true
true
204
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
If E5-CRD is a true ribonuclease that lacks His, which residues serve as the catalysts?
[ "32" ]
87
1,171
0
false
If E5-CRD is a true ribonuclease that lacks His, which residues serve as the catalysts?
[]
If E5-CRD is a true ribonuclease that lacks His, which residues serve as the catalysts?
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
Based on the crystal structure of the E5-CRD/dGpdUp complex, only Lys25, Lys60 and Arg33 were observed as charged residues with the proximity of the phosphates in the substrate (Figure 3B).
[ "32" ]
189
1,172
0
false
Based on the crystal structure of the E5-CRD/dGpdUp complex, only Lys25, Lys60 and Arg33 were observed as charged residues with the proximity of the phosphates in the substrate (Figure 3B).
[]
Based on the crystal structure of the E5-CRD/dGpdUp complex, only Lys25, Lys60 and Arg33 were observed as charged residues with the proximity of the phosphates in the substrate.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
With reference to the well-studied case of pancreatic RNase A in which His12 is a general base located close to 2′-OH and His119 is a general acid located close to 5′-O in the 2′,3′-cyclizing step (32), Arg33 may position itself corresponding to that of His12, and Lys25 or Lys60 may position itself corresponding to that of His119.
[ "32" ]
332
1,173
1
false
With reference to the well-studied case of pancreatic RNase A in which His12 is a general base located close to 2′-OH and His119 is a general acid located close to 5′-O in the 2′,3′-cyclizing step, Arg33 may position itself corresponding to that of His12, and Lys25 or Lys60 may position itself corresponding to that of His119.
[ "32" ]
With reference to the well-studied case of pancreatic RNase A in which His12 is a general base located close to 2′-OH and His119 is a general acid located close to 5′-O in the 2′,3′-cyclizing step, Arg33 may position itself corresponding to that of His12, and Lys25 or Lys60 may position itself corresponding to that of His119.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
The mutation analysis revealed that both R33Q and K25Q/K60Q mutants lost their killing activity, and either of the K25Q or the K60Q mutant exhibited a decreased activity.
[ "32" ]
170
1,174
0
false
The mutation analysis revealed that both R33Q and K25Q/K60Q mutants lost their killing activity, and either of the K25Q or the K60Q mutant exhibited a decreased activity.
[]
The mutation analysis revealed that both R33Q and K25Q/K60Q mutants lost their killing activity, and either of the K25Q or the K60Q mutant exhibited a decreased activity.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
Thus, this result suggests that these three basic residues are important for the catalytic activity.
[ "32" ]
100
1,175
0
false
Thus, this result suggests that these three basic residues are important for the catalytic activity.
[]
Thus, this result suggests that these three basic residues are important for the catalytic activity.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
Interestingly, E5-CRD preferred a very high pH to cleave a dinucleotide substrate (12).
[ "32" ]
87
1,176
0
false
Interestingly, E5-CRD preferred a very high pH to cleave a dinucleotide substrate (12).
[]
Interestingly, E5-CRD preferred a very high pH to cleave a dinucleotide substrate.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
The normally accepted pKa values of the Arg and Lys side chains might explain this unusual pH preference.
[ "32" ]
105
1,177
0
false
The normally accepted pKa values of the Arg and Lys side chains might explain this unusual pH preference.
[]
The normally accepted pKa values of the Arg and Lys side chains might explain this unusual pH preference.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
In addition, the carbonyl group of Ile94 is close to the guanidino group of Arg33, thereby forming a hydrogen bond; this possibly increases the basicity of the protonated guanidino group of Arg33.
[ "32" ]
196
1,178
0
false
In addition, the carbonyl group of Ile94 is close to the guanidino group of Arg33, thereby forming a hydrogen bond; this possibly increases the basicity of the protonated guanidino group of Arg33.
[]
In addition, the carbonyl group of Ile94 is close to the guanidino group of Arg33, thereby forming a hydrogen bond; this possibly increases the basicity of the protonated guanidino group of Arg33.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
However, we could not thoroughly measure the activity at higher pH values due to RNA instability.
[ "32" ]
97
1,179
0
false
However, we could not thoroughly measure the activity at higher pH values due to RNA instability.
[]
However, we could not thoroughly measure the activity at higher pH values due to RNA instability.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
On the other hand, in E.coli cells, in which it is difficult to achieve high pH values under physiological conditions, both Arg and Lys are assumed to be protonated.
[ "32" ]
165
1,180
0
false
On the other hand, in E.coli cells, in which it is difficult to achieve high pH values under physiological conditions, both Arg and Lys are assumed to be protonated.
[]
On the other hand, in E.coli cells, in which it is difficult to achieve high pH values under physiological conditions, both Arg and Lys are assumed to be protonated.
true
true
true
true
true
205
6
DISCUSSION
1
32
[ "b32" ]
17,099,236
pmid-11848924
Thus, it is unlikely for these basic residues to function as general acid–base catalysts.
[ "32" ]
89
1,181
0
false
Thus, it is unlikely for these basic residues to function as general acid–base catalysts.
[]
Thus, it is unlikely for these basic residues to function as general acid–base catalysts.
true
true
true
true
true
205
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
have reported the crystal structure of the apo form of E5-CRD; they showed that Asp54, Arg56, Lys59, Asp105 and Arg107 (corresponding to their residue numbers Asp46, Arg48, Lys51, Asp97 and Asp99, respectively) affected its ribonuclease activity due to mutations (20).
[ "20" ]
268
1,182
1
false
have reported the crystal structure of the apo form of E5-CRD; they showed that Asp54, Arg56, Lys59, Asp105 and Arg107 (corresponding to their residue numbers Asp46, Arg48, Lys51, Asp97 and Asp99, respectively) affected its ribonuclease activity due to mutations.
[ "20" ]
have reported the crystal structure of the apo form of E5-CRD; they showed that Asp54, Arg56, Lys59, Asp105 and Arg107 (corresponding to their residue numbers Asp46, Arg48, Lys51, Asp97 and Asp99, respectively) affected its ribonuclease activity due to mutations.
false
true
true
true
false
206
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
Further, among these residues, Asp54 and Arg56 were suggested to be putative catalytic residues.
[ "20" ]
96
1,183
0
false
Further, among these residues, Asp54 and Arg56 were suggested to be putative catalytic residues.
[]
Further, among these residues, Asp54 and Arg56 were suggested to be putative catalytic residues.
true
true
true
true
true
206
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
Based on the structure of our complex, however, the Cα atoms of Asp54 and Arg56 were located approximately 14 and 11 Å, respectively, apart from the 2′-C atom of the deoxyguanosine of dGpdUp; in addition, the residues were blocked by uridine thereby preventing their contact with the 2′-C atom and the phosphate group between dG and dU.
[ "20" ]
336
1,184
0
false
Based on the structure of our complex, however, the Cα atoms of Asp54 and Arg56 were located approximately 14 and 11 Å, respectively, apart from the 2′-C atom of the deoxyguanosine of dGpdUp; in addition, the residues were blocked by uridine thereby preventing their contact with the 2′-C atom and the phosphate group between dG and dU.
[]
Based on the structure of our complex, however, the Cα atoms of Asp54 and Arg56 were located approximately 14 and 11 Å, respectively, apart from the 2′-C atom of the deoxyguanosine of dGpdUp; in addition, the residues were blocked by uridine thereby preventing their contact with the 2′-C atom and the phosphate group between dG and dU.
true
true
true
true
true
206
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
Furthermore, instead of playing a role in substrate binding, Asp54 and Arg56 formed a salt bridge, enabling the complex structure to maintain its conformation.
[ "20" ]
159
1,185
0
false
Furthermore, instead of playing a role in substrate binding, Asp54 and Arg56 formed a salt bridge, enabling the complex structure to maintain its conformation.
[]
Furthermore, instead of playing a role in substrate binding, Asp54 and Arg56 formed a salt bridge, enabling the complex structure to maintain its conformation.
true
true
true
true
true
206
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
In addition, Asp105–Arg107 also formed a salt bridge, thereby contributing to the interaction with the uracil base ring of the substrate.
[ "20" ]
137
1,186
0
false
In addition, Asp105–Arg107 also formed a salt bridge, thereby contributing to the interaction with the uracil base ring of the substrate.
[]
In addition, Asp105–Arg107 also formed a salt bridge, thereby contributing to the interaction with the uracil base ring of the substrate.
true
true
true
true
true
206
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
Thus, the loss of the ribonuclease activity due to mutations of these two residues demonstrates their importance with regard to the uridine binding revealed by our structure.
[ "20" ]
174
1,187
0
false
Thus, the loss of the ribonuclease activity due to mutations of these two residues demonstrates their importance with regard to the uridine binding revealed by our structure.
[]
Thus, the loss of the ribonuclease activity due to mutations of these two residues demonstrates their importance with regard to the uridine binding revealed by our structure.
true
true
true
true
true
206
7
DISCUSSION
1
20
[ "b20" ]
17,099,236
pmid-16060658
Lys59 may also contribute to the substrate binding with the phosphate group.
[ "20" ]
76
1,188
0
false
Lys59 may also contribute to the substrate binding with the phosphate group.
[]
Lys59 may also contribute to the substrate binding with the phosphate group.
true
true
true
true
true
206
8
DISCUSSION
0
null
null
17,099,236
null
Therefore, the residues found in this study and by Lin et al.
null
61
1,189
0
false
null
null
Therefore, the residues found in this study and by Lin et al.
true
true
true
true
true
207
8
DISCUSSION
0
null
null
17,099,236
null
are crucial for the catalytic activity; however, none of these appear to be apparent catalytic residues, suggesting the existence of an alternative novel mechanism responsible for the E5 activity.
null
196
1,190
0
false
null
null
are crucial for the catalytic activity; however, none of these appear to be apparent catalytic residues, suggesting the existence of an alternative novel mechanism responsible for the E5 activity.
false
true
true
true
false
207
9
DISCUSSION
0
null
null
17,099,236
null
In deoxyribonucleases (DNases), a water molecule that is activated by divalent metal ions is involved in the catalytic reaction.
null
128
1,191
0
false
null
null
In deoxyribonucleases (DNases), a water molecule that is activated by divalent metal ions is involved in the catalytic reaction.
true
true
true
true
true
208
9
DISCUSSION
0
null
null
17,099,236
null
However, no metal ions were found to be associated with the E5-CRD/dGpdUp complex; in fact, the enzyme reaction was resistant to EDTA (data not shown).
null
151
1,192
0
false
null
null
However, no metal ions were found to be associated with the E5-CRD/dGpdUp complex; in fact, the enzyme reaction was resistant to EDTA (data not shown).
true
true
true
true
true
208
9
DISCUSSION
0
null
null
17,099,236
null
Although a water molecule was found to bind to O1P of the phosphate of dGpdUp in the active site, it may function to fix the substrate at the active site.
null
154
1,193
0
false
null
null
Although a water molecule was found to bind to O1P of the phosphate of dGpdUp in the active site, it may function to fix the substrate at the active site.
true
true
true
true
true
208
10
DISCUSSION
1
21
[ "b21", "b33" ]
17,099,236
pmid-16524591|pmid-8043575
Recently, Luna-Chávez et al.
[ "21", "33" ]
28
1,194
0
false
Recently, Luna-Chávez et al.
[]
Recently, Luna-Chávez et al.
true
true
true
true
true
209
10
DISCUSSION
1
21
[ "b21", "b33" ]
17,099,236
pmid-16524591|pmid-8043575
have solved the crystal structure of E5-CRD complexed with its cognate inhibitor protein ImmE5 through a multiwavelength anomalous diffraction experiment (21).
[ "21", "33" ]
159
1,195
1
false
have solved the crystal structure of E5-CRD complexed with its cognate inhibitor protein ImmE5 through a multiwavelength anomalous diffraction experiment.
[ "21" ]
have solved the crystal structure of E5-CRD complexed with its cognate inhibitor protein ImmE5 through a multiwavelength anomalous diffraction experiment.
false
true
true
true
false
209
10
DISCUSSION
1
21
[ "b21", "b33" ]
17,099,236
pmid-16524591|pmid-8043575
We have also been studying the same structure by using MIR.
[ "21", "33" ]
59
1,196
0
false
We have also been studying the same structure by using MIR.
[]
We have also been studying the same structure by using MIR.
true
true
true
true
true
209
10
DISCUSSION
1
21
[ "b21", "b33" ]
17,099,236
pmid-16524591|pmid-8043575
As a result, when we superposed our E5-CRD/ImmE5 structure onto the structure obtained by Luna-Chávez et al., the r.m.s.
[ "21", "33" ]
120
1,197
0
false
As a result, when we superposed our E5-CRD/ImmE5 structure onto the structure obtained by Luna-Chávez et al., the r.m.s.
[]
As a result, when we superposed our E5-CRD/ImmE5 structure onto the structure obtained by Luna-Chávez et al., the r.m.s.
true
true
true
true
true
209
10
DISCUSSION
1
21
[ "b21", "b33" ]
17,099,236
pmid-16524591|pmid-8043575
difference for the backbone atoms (Cα, C, O and N) was 0.18 Å.
[ "21", "33" ]
62
1,198
0
false
difference for the backbone atoms (Cα, C, O and N) was 0.18 Å.
[]
difference for the backbone atoms (Cα, C, O and N) was 0.18 Å.
false
true
true
true
false
209
10
DISCUSSION
1
21
[ "b21", "b33" ]
17,099,236
pmid-16524591|pmid-8043575
The resolutions of our structure and their structures are 1.9 and 1.15 Å, respectively.
[ "21", "33" ]
87
1,199
0
false
The resolutions of our structure and their structures are 1.9 and 1.15 Å, respectively.
[]
The resolutions of our structure and their structures are 1.9 and 1.15 Å, respectively.
true
true
true
true
true
209