Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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int64
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string
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int64
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
In our mapping experiments at php locus, transitions from a bubble to a Y arc were only detected in DNA fragments the most centered on the promoter region of php gene (Figure 2), which clearly demonstrated that replication initiates at a fixed origin linked to gene.
[ "26", "28", "32" ]
266
40,016
0
false
In our mapping experiments at php locus, transitions from a bubble to a Y arc were only detected in DNA fragments the most centered on the promoter region of php gene (Figure 2), which clearly demonstrated that replication initiates at a fixed origin linked to gene.
[]
In our mapping experiments at php locus, transitions from a bubble to a Y arc were only detected in DNA fragments the most centered on the promoter region of php gene, which clearly demonstrated that replication initiates at a fixed origin linked to gene.
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
Moreover, we did not find a mixture of bubble arc and complete Y arc throughout the S phase (Figure 1), indicating that the origin activation is efficient.
[ "26", "28", "32" ]
155
40,017
0
false
Moreover, we did not find a mixture of bubble arc and complete Y arc throughout the S phase (Figure 1), indicating that the origin activation is efficient.
[]
Moreover, we did not find a mixture of bubble arc and complete Y arc throughout the S phase (Figure 1), indicating that the origin activation is efficient.
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
Accordingly, the bubble arc signal did not result from a rare event, since it has also been detected in microplasmodia despite their asynchrony (Figure 5).
[ "26", "28", "32" ]
155
40,018
0
false
Accordingly, the bubble arc signal did not result from a rare event, since it has also been detected in microplasmodia despite their asynchrony (Figure 5).
[]
Accordingly, the bubble arc signal did not result from a rare event, since it has also been detected in microplasmodia despite their asynchrony (Figure 5).
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
Moreover, only the terminal portion of the Y arc was detected when analyzing this asynchronous population, showing the efficiency of origin firing.
[ "26", "28", "32" ]
147
40,019
0
false
Moreover, only the terminal portion of the Y arc was detected when analyzing this asynchronous population, showing the efficiency of origin firing.
[]
Moreover, only the terminal portion of the Y arc was detected when analyzing this asynchronous population, showing the efficiency of origin firing.
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
We also checked that no other origin was activated elsewhere within this locus in early S phase by determining replication fork directions (Figure 3).
[ "26", "28", "32" ]
150
40,020
0
false
We also checked that no other origin was activated elsewhere within this locus in early S phase by determining replication fork directions (Figure 3).
[]
We also checked that no other origin was activated elsewhere within this locus in early S phase by determining replication fork directions (Figure 3).
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
In addition, 2D-gel analyses of overlapping restriction fragments spanning 21 kb around the gene did not show other initiation events or termination during S phase (Figure 2; data not shown).
[ "26", "28", "32" ]
191
40,021
0
false
In addition, 2D-gel analyses of overlapping restriction fragments spanning 21 kb around the gene did not show other initiation events or termination during S phase (Figure 2; data not shown).
[]
In addition, 2D-gel analyses of overlapping restriction fragments spanning 21 kb around the gene did not show other initiation events or termination during S phase.
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
These results argue for an efficient activation of a localized origin.
[ "26", "28", "32" ]
70
40,022
0
false
These results argue for an efficient activation of a localized origin.
[]
These results argue for an efficient activation of a localized origin.
true
true
true
true
true
6,910
5
DISCUSSION
1
26
[ "B26", "B28", "B32" ]
17,717,000
pmid-1630902|NA|pmid-10219081
Such origins have been described before in Physarum (26,28,32), indicating that stochastic firing is not the rule in this organism.
[ "26", "28", "32" ]
131
40,023
0
false
Such origins have been described before in Physarum, indicating that stochastic firing is not the rule in this organism.
[ "26,28,32" ]
Such origins have been described before in Physarum, indicating that stochastic firing is not the rule in this organism.
true
true
true
true
true
6,910
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
However, we detected a faint bubble arc signal from +10 min to +60 min (Figure 1).
[ "28", "32", "47" ]
82
40,024
0
false
However, we detected a faint bubble arc signal from +10 min to +60 min (Figure 1).
[]
However, we detected a faint bubble arc signal from +10 min to +60 min (Figure 1).
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
In vivo HU treatment from +60 to +90 min showed that forks forming this bubble arc were still active at +60 min since the drug treatment delayed replication pattern (Figure 6).
[ "28", "32", "47" ]
176
40,025
0
false
In vivo HU treatment from +60 to +90 min showed that forks forming this bubble arc were still active at +60 min since the drug treatment delayed replication pattern (Figure 6).
[]
In vivo HU treatment from +60 to +90 min showed that forks forming this bubble arc were still active at +60 min since the drug treatment delayed replication pattern (Figure 6).
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
These observations can be related to the low intensity of replication signals at the beginning of S phase, following 2D-gel and denaturing gel analyses (Figures 1 and 4).
[ "28", "32", "47" ]
170
40,026
0
false
These observations can be related to the low intensity of replication signals at the beginning of S phase, following 2D-gel and denaturing gel analyses (Figures 1 and 4).
[]
These observations can be related to the low intensity of replication signals at the beginning of S phase, following 2D-gel and denaturing gel analyses (Figures 1 and 4).
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
Altogether, these results suggest a delayed activation of the origin in a small part of the nuclei contained within a plasmodium or they reflect different replication patterns of the two alleles contained within each nucleus.
[ "28", "32", "47" ]
225
40,027
0
false
Altogether, these results suggest a delayed activation of the origin in a small part of the nuclei contained within a plasmodium or they reflect different replication patterns of the two alleles contained within each nucleus.
[]
Altogether, these results suggest a delayed activation of the origin in a small part of the nuclei contained within a plasmodium or they reflect different replication patterns of the two alleles contained within each nucleus.
true
true
true
true
true
6,911
6
DISCUSSION
1
47
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
Although our previous studies have clearly shown a concerted activation of allelic origins at other loci (28,32), such a different replication pattern between two alleles has been already described in Physarum (47).
[ "28", "32", "47" ]
215
40,028
1
false
Although our previous studies have clearly shown a concerted activation of allelic origins at other loci, such a different replication pattern between two alleles has been already described in Physarum.
[ "28,32", "47" ]
Although our previous studies have clearly shown a concerted activation of allelic origins at other loci, such a different replication pattern between two alleles has been already described in Physarum.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
From a gene dosage analysis, the authors found that the 2 allelic altB1 and altB2 alpha-tubulin loci replicate synchronously in early S phase, while altA locus replicates later.
[ "28", "32", "47" ]
177
40,029
0
false
From a gene dosage analysis, the authors found that the 2 allelic altB1 and altB2 alpha-tubulin loci replicate synchronously in early S phase, while altA locus replicates later.
[]
From a gene dosage analysis, the authors found that the 2 allelic altB1 and altB2 alpha-tubulin loci replicate synchronously in early S phase, while altA locus replicates later.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
Remarkably, altA2 allele replicates in a prolonged period of mid-S phase and asynchronously from altA1 allele, which replicates earlier.
[ "28", "32", "47" ]
136
40,030
0
false
Remarkably, altA2 allele replicates in a prolonged period of mid-S phase and asynchronously from altA1 allele, which replicates earlier.
[]
Remarkably, altA2 allele replicates in a prolonged period of mid-S phase and asynchronously from altA1 allele, which replicates earlier.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
In this view, for php locus, we can hypothesize simultaneous early activation of one allelic origin in all nuclei, while the other is activated progressively throughout the first hour of the S phase.
[ "28", "32", "47" ]
199
40,031
0
false
In this view, for php locus, we can hypothesize simultaneous early activation of one allelic origin in all nuclei, while the other is activated progressively throughout the first hour of the S phase.
[]
In this view, for php locus, we can hypothesize simultaneous early activation of one allelic origin in all nuclei, while the other is activated progressively throughout the first hour of the S phase.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
Such distinct patterns of replication of the alleles were not obvious on 2D-gel.
[ "28", "32", "47" ]
80
40,032
0
false
Such distinct patterns of replication of the alleles were not obvious on 2D-gel.
[]
Such distinct patterns of replication of the alleles were not obvious on 2D-gel.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
However individual quantification of allelic RI signals is not significant when allelic fragments are of a similar size.
[ "28", "32", "47" ]
120
40,033
0
false
However individual quantification of allelic RI signals is not significant when allelic fragments are of a similar size.
[]
However individual quantification of allelic RI signals is not significant when allelic fragments are of a similar size.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
Furthermore, we did not find a restriction fragment length polymorphism that would allow unambiguous distinguishing of the replication timing of the two alleles.
[ "28", "32", "47" ]
161
40,034
0
false
Furthermore, we did not find a restriction fragment length polymorphism that would allow unambiguous distinguishing of the replication timing of the two alleles.
[]
Furthermore, we did not find a restriction fragment length polymorphism that would allow unambiguous distinguishing of the replication timing of the two alleles.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
In these conditions, it is not clear whether php alleles are replicating exactly synchronously or not.
[ "28", "32", "47" ]
102
40,035
0
false
In these conditions, it is not clear whether php alleles are replicating exactly synchronously or not.
[]
In these conditions, it is not clear whether php alleles are replicating exactly synchronously or not.
true
true
true
true
true
6,911
6
DISCUSSION
1
28
[ "B28", "B32", "B47" ]
17,717,000
NA|pmid-10219081|pmid-8093328
Nonetheless a delayed activation of php origin certainly occurs in a non-negligible number of molecules.
[ "28", "32", "47" ]
104
40,036
0
false
Nonetheless a delayed activation of php origin certainly occurs in a non-negligible number of molecules.
[]
Nonetheless a delayed activation of php origin certainly occurs in a non-negligible number of molecules.
true
true
true
true
true
6,911
7
DISCUSSION
1
15
[ "B15", "B16", "B48", "B49", "B26", "B28", "B32" ]
17,717,000
pmid-12776736|pmid-16307921|pmid-16845368|pmid-6217973|pmid-1630902|NA|pmid-10219081
php origin is developmentally regulated and origin activation correlates with php transcriptional activity (Figure 7).
[ "15", "16", "48", "49", "26", "28", "32" ]
118
40,037
0
false
php origin is developmentally regulated and origin activation correlates with php transcriptional activity (Figure 7).
[]
php origin is developmentally regulated and origin activation correlates with php transcriptional activity (Figure 7).
false
true
true
true
false
6,912
7
DISCUSSION
1
15
[ "B15", "B16", "B48", "B49", "B26", "B28", "B32" ]
17,717,000
pmid-12776736|pmid-16307921|pmid-16845368|pmid-6217973|pmid-1630902|NA|pmid-10219081
Such a modulation of origin firing has been previously reported for proA and proP loci in Physarum (15) and has also been described in other organisms (16,48).
[ "15", "16", "48", "49", "26", "28", "32" ]
159
40,038
1
false
Such a modulation of origin firing has been previously reported for proA and proP loci in Physarum and has also been described in other organisms.
[ "15", "16,48" ]
Such a modulation of origin firing has been previously reported for proA and proP loci in Physarum and has also been described in other organisms.
true
true
true
true
true
6,912
7
DISCUSSION
1
15
[ "B15", "B16", "B48", "B49", "B26", "B28", "B32" ]
17,717,000
pmid-12776736|pmid-16307921|pmid-16845368|pmid-6217973|pmid-1630902|NA|pmid-10219081
These observations indicate that eukaryotic origins are at least in part epigenetically defined and suggest a strong correlation between replication and transcription.
[ "15", "16", "48", "49", "26", "28", "32" ]
167
40,039
0
false
These observations indicate that eukaryotic origins are at least in part epigenetically defined and suggest a strong correlation between replication and transcription.
[]
These observations indicate that eukaryotic origins are at least in part epigenetically defined and suggest a strong correlation between replication and transcription.
true
true
true
true
true
6,912
7
DISCUSSION
1
49
[ "B15", "B16", "B48", "B49", "B26", "B28", "B32" ]
17,717,000
pmid-12776736|pmid-16307921|pmid-16845368|pmid-6217973|pmid-1630902|NA|pmid-10219081
This relationship has been previously observed on chromatin spreads from early S phase plasmodia: electron microscope investigation showed a tight linkage between active genes and early firing origins (49).
[ "15", "16", "48", "49", "26", "28", "32" ]
206
40,040
1
false
This relationship has been previously observed on chromatin spreads from early S phase plasmodia: electron microscope investigation showed a tight linkage between active genes and early firing origins.
[ "49" ]
This relationship has been previously observed on chromatin spreads from early S phase plasmodia: electron microscope investigation showed a tight linkage between active genes and early firing origins.
true
true
true
true
true
6,912
7
DISCUSSION
1
15
[ "B15", "B16", "B48", "B49", "B26", "B28", "B32" ]
17,717,000
pmid-12776736|pmid-16307921|pmid-16845368|pmid-6217973|pmid-1630902|NA|pmid-10219081
At the level of individual genes, we confirmed by 2D-gel mapping that efficient early firing origins are situated in the vicinity of abundantly transcribed genes.
[ "15", "16", "48", "49", "26", "28", "32" ]
162
40,041
0
false
At the level of individual genes, we confirmed by 2D-gel mapping that efficient early firing origins are situated in the vicinity of abundantly transcribed genes.
[]
At the level of individual genes, we confirmed by 2D-gel mapping that efficient early firing origins are situated in the vicinity of abundantly transcribed genes.
true
true
true
true
true
6,912
7
DISCUSSION
1
15
[ "B15", "B16", "B48", "B49", "B26", "B28", "B32" ]
17,717,000
pmid-12776736|pmid-16307921|pmid-16845368|pmid-6217973|pmid-1630902|NA|pmid-10219081
This was demonstrated for the constitutively expressed ardB and ardC actin genes, the developmentally regulated proP profilin gene and the cell cycle regulated H4-1 and H4-2 histone genes (26,28,32).
[ "15", "16", "48", "49", "26", "28", "32" ]
199
40,042
0
false
This was demonstrated for the constitutively expressed ardB and ardC actin genes, the developmentally regulated proP profilin gene and the cell cycle regulated H4-1 and H4-2 histone genes.
[ "26,28,32" ]
This was demonstrated for the constitutively expressed ardB and ardC actin genes, the developmentally regulated proP profilin gene and the cell cycle regulated H4-1 and H4-2 histone genes.
true
true
true
true
true
6,912
8
DISCUSSION
1
15
[ "B15", "B26", "B34", "B34" ]
17,717,000
pmid-12776736|pmid-1630902|pmid-12034812|pmid-12034812
In contrast, studies of weakly expressed genes revealed that they are replicated with different patterns.
[ "15", "26", "34", "34" ]
105
40,043
0
false
In contrast, studies of weakly expressed genes revealed that they are replicated with different patterns.
[]
In contrast, studies of weakly expressed genes revealed that they are replicated with different patterns.
true
true
true
true
true
6,913
8
DISCUSSION
1
15
[ "B15", "B26", "B34", "B34" ]
17,717,000
pmid-12776736|pmid-1630902|pmid-12034812|pmid-12034812
Inactive proA profilin gene is passively replicated in mid-S phase (15,26).
[ "15", "26", "34", "34" ]
75
40,044
0
false
Inactive proA profilin gene is passively replicated in mid-S phase.
[ "15,26" ]
Inactive proA profilin gene is passively replicated in mid-S phase.
true
true
true
true
true
6,913
8
DISCUSSION
1
15
[ "B15", "B26", "B34", "B34" ]
17,717,000
pmid-12776736|pmid-1630902|pmid-12034812|pmid-12034812
The weakly expressed redB and redE and topoisomerase II genes are replicated early in S phase since they are embedded in a cluster of early-activated replicons
[ "15", "26", "34", "34" ]
159
40,045
0
false
The weakly expressed redB and redE and topoisomerase II genes are replicated early in S phase since they are embedded in a cluster of early-activated replicons
[]
The weakly expressed redB and redE and topoisomerase II genes are replicated early in S phase since they are embedded in a cluster of early-activated replicons
true
true
false
true
false
6,913
8
DISCUSSION
1
15
[ "B15", "B26", "B34", "B34" ]
17,717,000
pmid-12776736|pmid-1630902|pmid-12034812|pmid-12034812
[(34), unpublished data].
[ "15", "26", "34", "34" ]
25
40,046
0
false
.
[ "(34), unpublished data" ]
.
false
false
true
true
false
6,913
8
DISCUSSION
1
15
[ "B15", "B26", "B34", "B34" ]
17,717,000
pmid-12776736|pmid-1630902|pmid-12034812|pmid-12034812
Yet, in these cases, the genes are not coincident with an origin but with a termination site.
[ "15", "26", "34", "34" ]
93
40,047
0
false
Yet, in these cases, the genes are not coincident with an origin but with a termination site.
[]
Yet, in these cases, the genes are not coincident with an origin but with a termination site.
true
true
true
true
true
6,913
8
DISCUSSION
1
34
[ "B15", "B26", "B34", "B34" ]
17,717,000
pmid-12776736|pmid-1630902|pmid-12034812|pmid-12034812
Finally, the redA gene contains a replication origin in the promoter region, but this origin inefficiently fires in a large temporal window of mid-S phase (34).
[ "15", "26", "34", "34" ]
160
40,048
1
false
Finally, the redA gene contains a replication origin in the promoter region, but this origin inefficiently fires in a large temporal window of mid-S phase.
[ "34" ]
Finally, the redA gene contains a replication origin in the promoter region, but this origin inefficiently fires in a large temporal window of mid-S phase.
true
true
true
true
true
6,913
9
DISCUSSION
1
50
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
Therefore, the association of an efficient early origin with a transcriptional promoter might be a unique property of highly expressed genes in Physarum.
[ "50", "51", "52", "53", "48", "53" ]
153
40,049
0
false
Therefore, the association of an efficient early origin with a transcriptional promoter might be a unique property of highly expressed genes in Physarum.
[]
Therefore, the association of an efficient early origin with a transcriptional promoter might be a unique property of highly expressed genes in Physarum.
true
true
true
true
true
6,914
9
DISCUSSION
1
50
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
It remains to be determined whether the origins surrounding redB, redE and topoisomerase II genes could be coincident with active genes.
[ "50", "51", "52", "53", "48", "53" ]
136
40,050
0
false
It remains to be determined whether the origins surrounding redB, redE and topoisomerase II genes could be coincident with active genes.
[]
It remains to be determined whether the origins surrounding redB, redE and topoisomerase II genes could be coincident with active genes.
true
true
true
true
true
6,914
9
DISCUSSION
1
50
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
Likewise, the transcriptional status of the php locus is unknown; it would be of interest to investigate it in the region where replication forks are stalling.
[ "50", "51", "52", "53", "48", "53" ]
159
40,051
0
false
Likewise, the transcriptional status of the php locus is unknown; it would be of interest to investigate it in the region where replication forks are stalling.
[]
Likewise, the transcriptional status of the php locus is unknown; it would be of interest to investigate it in the region where replication forks are stalling.
true
true
true
true
true
6,914
9
DISCUSSION
1
50
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
In metazoan, co-localization of active genes and origins has been often found and suggests that replication and transcription may share common regulation, perhaps as chromatin domain units (50,51).
[ "50", "51", "52", "53", "48", "53" ]
197
40,052
0
false
In metazoan, co-localization of active genes and origins has been often found and suggests that replication and transcription may share common regulation, perhaps as chromatin domain units.
[ "50,51" ]
In metazoan, co-localization of active genes and origins has been often found and suggests that replication and transcription may share common regulation, perhaps as chromatin domain units.
true
true
true
true
true
6,914
9
DISCUSSION
1
52
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
Several examples of origin specification in relation with transcription have been described at various loci like rRNA genes in Xenopus embryos (52), DHFR locus in hamster cells (53) and Hox genes in mouse cells (48).
[ "50", "51", "52", "53", "48", "53" ]
216
40,053
1
false
Several examples of origin specification in relation with transcription have been described at various loci like rRNA genes in Xenopus embryos, DHFR locus in hamster cells and Hox genes in mouse cells.
[ "52", "53", "48" ]
Several examples of origin specification in relation with transcription have been described at various loci like rRNA genes in Xenopus embryos, DHFR locus in hamster cells and Hox genes in mouse cells.
true
true
true
true
true
6,914
9
DISCUSSION
1
53
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
In addition, deletion of DHFR promoter results in a modification of replication initiation activity at this locus (53).
[ "50", "51", "52", "53", "48", "53" ]
119
40,054
1
false
In addition, deletion of DHFR promoter results in a modification of replication initiation activity at this locus.
[ "53" ]
In addition, deletion of DHFR promoter results in a modification of replication initiation activity at this locus.
true
true
true
true
true
6,914
9
DISCUSSION
1
50
[ "B50", "B51", "B52", "B53", "B48", "B53" ]
17,717,000
pmid-14731611|pmid-11483989|pmid-7481806|pmid-14977920|pmid-16845368|pmid-14977920
This again suggests a coupling of these two nuclear activities.
[ "50", "51", "52", "53", "48", "53" ]
63
40,055
0
false
This again suggests a coupling of these two nuclear activities.
[]
This again suggests a coupling of these two nuclear activities.
true
true
true
true
true
6,914
10
DISCUSSION
0
null
null
17,717,000
null
In this light, we propose that the replication of highly expressed genes is strictly regulated in Physarum.
null
107
40,056
0
false
null
null
In this light, we propose that the replication of highly expressed genes is strictly regulated in Physarum.
true
true
true
true
true
6,915
10
DISCUSSION
0
null
null
17,717,000
null
This tight control would involve the location of the active genes close to very early firing replication origins.
null
113
40,057
0
false
null
null
This tight control would involve the location of the active genes close to very early firing replication origins.
true
true
true
true
true
6,915
10
DISCUSSION
0
null
null
17,717,000
null
Lower expressed loci or non-coding regions would be under a more relax control, so that the replication timing would be less defined or the origin efficiency would be reduced.
null
175
40,058
0
false
null
null
Lower expressed loci or non-coding regions would be under a more relax control, so that the replication timing would be less defined or the origin efficiency would be reduced.
true
true
true
true
true
6,915
10
DISCUSSION
0
null
null
17,717,000
null
The replication organization of php locus may illustrate a transition in replication control stringency related with transcription level.
null
137
40,059
0
false
null
null
The replication organization of php locus may illustrate a transition in replication control stringency related with transcription level.
true
true
true
true
true
6,915
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6", "B7", "B8" ]
20,047,964
NA|pmid-1989886|pmid-1989882|pmid-6088516|pmid-16188275|pmid-10194386|pmid-15770420|pmid-12437341|pmid-11839309|pmid-15165852|pmid-15165852|pmid-12470949|pmid-15111055|pmid-15920477
The nucleases that cleave the phosphodiester backbone of DNA to leave 5′-phosphate and 3′-hydroxyl termini participate in many varied biological processes, including DNA replication, repair, recombination, immunity, defence and apoptosis.
[ "1", "2", "3", "4–6", "7", "8" ]
238
40,060
0
false
The nucleases that cleave the phosphodiester backbone of DNA to leave 5′-phosphate and 3′-hydroxyl termini participate in many varied biological processes, including DNA replication, repair, recombination, immunity, defence and apoptosis.
[]
The nucleases that cleave the phosphodiester backbone of DNA to leave 5′-phosphate and 3′-hydroxyl termini participate in many varied biological processes, including DNA replication, repair, recombination, immunity, defence and apoptosis.
true
true
true
true
true
6,916
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6", "B7", "B8" ]
20,047,964
NA|pmid-1989886|pmid-1989882|pmid-6088516|pmid-16188275|pmid-10194386|pmid-15770420|pmid-12437341|pmid-11839309|pmid-15165852|pmid-15165852|pmid-12470949|pmid-15111055|pmid-15920477
The vast majority of nucleases use divalent metal ions as cofactors, though the number and identity of the ions can differ (1).
[ "1", "2", "3", "4–6", "7", "8" ]
127
40,061
1
false
The vast majority of nucleases use divalent metal ions as cofactors, though the number and identity of the ions can differ.
[ "1" ]
The vast majority of nucleases use divalent metal ions as cofactors, though the number and identity of the ions can differ.
true
true
true
true
true
6,916
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6", "B7", "B8" ]
20,047,964
NA|pmid-1989886|pmid-1989882|pmid-6088516|pmid-16188275|pmid-10194386|pmid-15770420|pmid-12437341|pmid-11839309|pmid-15165852|pmid-15165852|pmid-12470949|pmid-15111055|pmid-15920477
The presence of two divalent metal ions in the active site of the 3′-5′ exonuclease domain of Escherichia coli DNA polymerase I led Steitz and co-workers to propose a reaction mechanism in which a water molecule from the coordination sphere of the first metal ion performs an in-line nucleophilic attack on the scissile ...
[ "1", "2", "3", "4–6", "7", "8" ]
422
40,062
0
false
The presence of two divalent metal ions in the active site of the 3′-5′ exonuclease domain of Escherichia coli DNA polymerase I led Steitz and co-workers to propose a reaction mechanism in which a water molecule from the coordination sphere of the first metal ion performs an in-line nucleophilic attack on the scissile ...
[ "2,3" ]
The presence of two divalent metal ions in the active site of the 3′-5′ exonuclease domain of Escherichia coli DNA polymerase I led Steitz and co-workers to propose a reaction mechanism in which a water molecule from the coordination sphere of the first metal ion performs an in-line nucleophilic attack on the scissile ...
true
true
true
true
true
6,916
0
INTRODUCTION
1
4–6
[ "B1", "B2", "B3", "B4 B5 B6", "B7", "B8" ]
20,047,964
NA|pmid-1989886|pmid-1989882|pmid-6088516|pmid-16188275|pmid-10194386|pmid-15770420|pmid-12437341|pmid-11839309|pmid-15165852|pmid-15165852|pmid-12470949|pmid-15111055|pmid-15920477
The single step reaction proceeds with inversion of configuration at the scissile phosphate (4–6).
[ "1", "2", "3", "4–6", "7", "8" ]
98
40,063
1
false
The single step reaction proceeds with inversion of configuration at the scissile phosphate.
[ "4–6" ]
The single step reaction proceeds with inversion of configuration at the scissile phosphate.
true
true
true
true
true
6,916
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6", "B7", "B8" ]
20,047,964
NA|pmid-1989886|pmid-1989882|pmid-6088516|pmid-16188275|pmid-10194386|pmid-15770420|pmid-12437341|pmid-11839309|pmid-15165852|pmid-15165852|pmid-12470949|pmid-15111055|pmid-15920477
Many of metal-dependent nucleases that generate double-strand breaks in DNA feature two identical subunits related by 2-fold symmetry.
[ "1", "2", "3", "4–6", "7", "8" ]
134
40,064
0
false
Many of metal-dependent nucleases that generate double-strand breaks in DNA feature two identical subunits related by 2-fold symmetry.
[]
Many of metal-dependent nucleases that generate double-strand breaks in DNA feature two identical subunits related by 2-fold symmetry.
true
true
true
true
true
6,916
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6", "B7", "B8" ]
20,047,964
NA|pmid-1989886|pmid-1989882|pmid-6088516|pmid-16188275|pmid-10194386|pmid-15770420|pmid-12437341|pmid-11839309|pmid-15165852|pmid-15165852|pmid-12470949|pmid-15111055|pmid-15920477
Each subunit contains a single active site: one catalyzes the cleavage of the scissile phosphodiester bond in the 3′–5′ strand and the other the equivalent bond in the 5′–3′ strand (7,8).
[ "1", "2", "3", "4–6", "7", "8" ]
187
40,065
0
false
Each subunit contains a single active site: one catalyzes the cleavage of the scissile phosphodiester bond in the 3′–5′ strand and the other the equivalent bond in the 5′–3′ strand.
[ "7,8" ]
Each subunit contains a single active site: one catalyzes the cleavage of the scissile phosphodiester bond in the 3′–5′ strand and the other the equivalent bond in the 5′–3′ strand.
true
true
true
true
true
6,916
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
DNA nucleases of the phospholipase D (PLD) superfamily use a different mechanism for the hydrolysis of phosphodiester bonds, a two-step metal-independent scheme (9,10).
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
168
40,066
0
false
DNA nucleases of the phospholipase D (PLD) superfamily use a different mechanism for the hydrolysis of phosphodiester bonds, a two-step metal-independent scheme.
[ "9,10" ]
DNA nucleases of the phospholipase D (PLD) superfamily use a different mechanism for the hydrolysis of phosphodiester bonds, a two-step metal-independent scheme.
true
true
true
true
true
6,917
1
INTRODUCTION
1
11
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
The two-step scheme is conserved throughout the PLD superfamily, a large and diverse group of proteins that includes plant, mammalian and bacterial phospholipases, phospholipid synthases, bacterial toxins and poxvirus envelope proteins (11).
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
241
40,067
1
false
The two-step scheme is conserved throughout the PLD superfamily, a large and diverse group of proteins that includes plant, mammalian and bacterial phospholipases, phospholipid synthases, bacterial toxins and poxvirus envelope proteins.
[ "11" ]
The two-step scheme is conserved throughout the PLD superfamily, a large and diverse group of proteins that includes plant, mammalian and bacterial phospholipases, phospholipid synthases, bacterial toxins and poxvirus envelope proteins.
true
true
true
true
true
6,917
1
INTRODUCTION
1
11
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
All PLD enzymes contain two copies of a conserved sequence motif ‘HXK’; both copies contribute to the active site (11).
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
119
40,068
1
false
All PLD enzymes contain two copies of a conserved sequence motif ‘HXK’; both copies contribute to the active site.
[ "11" ]
All PLD enzymes contain two copies of a conserved sequence motif ‘HXK’; both copies contribute to the active site.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
In some instances, such as the PLD from Streptomyces species and human tyrosyl-DNA phosphodiesterase 1 (Tdp1), the enzyme is a monomeric protein with two domains, which each carry one ‘HXK’ motif that together form the active site (Figure 1A)
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
242
40,069
0
false
In some instances, such as the PLD from Streptomyces species and human tyrosyl-DNA phosphodiesterase 1 (Tdp1), the enzyme is a monomeric protein with two domains, which each carry one ‘HXK’ motif that together form the active site (Figure 1A)
[]
In some instances, such as the PLD from Streptomyces species and human tyrosyl-DNA phosphodiesterase 1 (Tdp1), the enzyme is a monomeric protein with two domains, which each carry one ‘HXK’ motif that together form the active site (Figure 1A)
true
true
false
true
false
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
In contrast, the non-specific endonuclease Nuc, the restriction endonuclease BfiI and human mitochondrial phospholipase all have one ‘HXK’ motif per protein chain but form dimers with a single active site at the subunit interface that contains the ‘HXK’ motifs from both subunits (Figure 1A) (10,14,15).
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
303
40,070
0
false
In contrast, the non-specific endonuclease Nuc, the restriction endonuclease BfiI and human mitochondrial phospholipase all have one ‘HXK’ motif per protein chain but form dimers with a single active site at the subunit interface that contains the ‘HXK’ motifs from both subunits (Figure 1A).
[ "10,14,15" ]
In contrast, the non-specific endonuclease Nuc, the restriction endonuclease BfiI and human mitochondrial phospholipase all have one ‘HXK’ motif per protein chain but form dimers with a single active site at the subunit interface that contains the ‘HXK’ motifs from both subunits (Figure 1A).
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
The histidine residues of the two ‘HXK’ motifs play key roles in catalysis by PLD enzymes (10,13,16).
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
101
40,071
0
false
The histidine residues of the two ‘HXK’ motifs play key roles in catalysis by PLD enzymes.
[ "10,13,16" ]
The histidine residues of the two ‘HXK’ motifs play key roles in catalysis by PLD enzymes.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
A His from one ‘HXK’ motif acts as the nucleophile that attacks the scissile phosphate to create a covalent phosphohistidine intermediate, while that from the second ‘HXK’ motif stabilizes the leaving group.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
207
40,072
0
false
A His from one ‘HXK’ motif acts as the nucleophile that attacks the scissile phosphate to create a covalent phosphohistidine intermediate, while that from the second ‘HXK’ motif stabilizes the leaving group.
[]
A His from one ‘HXK’ motif acts as the nucleophile that attacks the scissile phosphate to create a covalent phosphohistidine intermediate, while that from the second ‘HXK’ motif stabilizes the leaving group.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
In a monomeric PLD protein, the two active-site histidines are not equivalent and each plays a defined role in catalysis.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
121
40,073
0
false
In a monomeric PLD protein, the two active-site histidines are not equivalent and each plays a defined role in catalysis.
[]
In a monomeric PLD protein, the two active-site histidines are not equivalent and each plays a defined role in catalysis.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
Conversely, the active sites of the homodimeric nucleases, BfiI and Nuc, contain two identical histidines related by 2-fold symmetry, one from each subunit.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
156
40,074
0
false
Conversely, the active sites of the homodimeric nucleases, BfiI and Nuc, contain two identical histidines related by 2-fold symmetry, one from each subunit.
[]
Conversely, the active sites of the homodimeric nucleases, BfiI and Nuc, contain two identical histidines related by 2-fold symmetry, one from each subunit.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
Figure 1.Enzymes of the phospholipase D superfamily.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
52
40,075
0
false
Figure 1.Enzymes of the phospholipase D superfamily.
[]
Figure 1.Enzymes of the phospholipase D superfamily.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
Monomeric and homodimeric PLD enzymes.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
38
40,076
0
false
Monomeric and homodimeric PLD enzymes.
[]
Monomeric and homodimeric PLD enzymes.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
The single PLD domain in the dimeric enzymes is depicted as a white circle, and the two domains in the monomeric enzymes as a circle and a hexagon.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
147
40,077
0
false
The single PLD domain in the dimeric enzymes is depicted as a white circle, and the two domains in the monomeric enzymes as a circle and a hexagon.
[]
The single PLD domain in the dimeric enzymes is depicted as a white circle, and the two domains in the monomeric enzymes as a circle and a hexagon.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
The DNA recognition domains of BfiI are marked as shaded diamonds.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
66
40,078
0
false
The DNA recognition domains of BfiI are marked as shaded diamonds.
[]
The DNA recognition domains of BfiI are marked as shaded diamonds.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
Both types of enzymes contain a single active site at the domain or subunit interface (marked by an asterisk).
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
110
40,079
0
false
Both types of enzymes contain a single active site at the domain or subunit interface (marked by an asterisk).
[]
Both types of enzymes contain a single active site at the domain or subunit interface (marked by an asterisk).
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
The putative reaction mechanism of BfiI.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
40
40,080
0
false
The putative reaction mechanism of BfiI.
[]
The putative reaction mechanism of BfiI.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
During the first step of the reaction, His105 from subunit A (H105:A) attacks the scissile phosphate to generate the covalent intermediate, while His105 from subunit B (H105:B) protonates the 3′-leaving group.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
209
40,081
0
false
During the first step of the reaction, His105 from subunit A attacks the scissile phosphate to generate the covalent intermediate, while His105 from subunit B protonates the 3′-leaving group.
[ "H105:A", "H105:B" ]
During the first step of the reaction, His105 from subunit A attacks the scissile phosphate to generate the covalent intermediate, while His105 from subunit B protonates the 3′-leaving group.
true
true
true
true
true
6,917
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B11", "B12", "B13", "B10", "B14", "B15", "B10", "B13", "B16" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-8732763|pmid-8732763|pmid-11839309|pmid-15165852|pmid-10074947|pmid-16247004|pmid-17028579|pmid-10074947|pmid-15165852|pmid-12470949|pmid-10074947|pmid-16247004
During the second step, a water molecule resolves the covalent intermediate releasing the first histidine (H105:A); the second histidine (H105:B) may facilitate this reaction by subtracting a proton from the water molecule.
[ "9", "10", "11", "11", "12", "13", "10", "14", "15", "10", "13", "16" ]
223
40,082
0
false
During the second step, a water molecule resolves the covalent intermediate releasing the first histidine ; the second histidine may facilitate this reaction by subtracting a proton from the water molecule.
[ "H105:A", "H105:B" ]
During the second step, a water molecule resolves the covalent intermediate releasing the first histidine ; the second histidine may facilitate this reaction by subtracting a proton from the water molecule.
true
true
true
true
true
6,917
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
Enzymes of the phospholipase D superfamily.
null
43
40,083
0
false
null
null
Enzymes of the phospholipase D superfamily.
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
Monomeric and homodimeric PLD enzymes.
null
38
40,084
0
false
null
null
Monomeric and homodimeric PLD enzymes.
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
The single PLD domain in the dimeric enzymes is depicted as a white circle, and the two domains in the monomeric enzymes as a circle and a hexagon.
null
147
40,085
0
false
null
null
The single PLD domain in the dimeric enzymes is depicted as a white circle, and the two domains in the monomeric enzymes as a circle and a hexagon.
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
The DNA recognition domains of BfiI are marked as shaded diamonds.
null
66
40,086
0
false
null
null
The DNA recognition domains of BfiI are marked as shaded diamonds.
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
Both types of enzymes contain a single active site at the domain or subunit interface (marked by an asterisk).
null
110
40,087
0
false
null
null
Both types of enzymes contain a single active site at the domain or subunit interface (marked by an asterisk).
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
The putative reaction mechanism of BfiI.
null
40
40,088
0
false
null
null
The putative reaction mechanism of BfiI.
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
During the first step of the reaction, His105 from subunit A (H105:A) attacks the scissile phosphate to generate the covalent intermediate, while His105 from subunit B (H105:B) protonates the 3′-leaving group.
null
209
40,089
0
false
null
null
During the first step of the reaction, His105 from subunit A (H105:A) attacks the scissile phosphate to generate the covalent intermediate, while His105 from subunit B (H105:B) protonates the 3′-leaving group.
true
true
true
true
true
6,918
2
INTRODUCTION
0
null
null
20,047,964
NA|pmid-16188275|NA|pmid-1550825|pmid-16188275|NA
During the second step, a water molecule resolves the covalent intermediate releasing the first histidine (H105:A); the second histidine (H105:B) may facilitate this reaction by subtracting a proton from the water molecule.
null
223
40,090
0
false
null
null
During the second step, a water molecule resolves the covalent intermediate releasing the first histidine (H105:A); the second histidine (H105:B) may facilitate this reaction by subtracting a proton from the water molecule.
true
true
true
true
true
6,918
3
INTRODUCTION
0
null
null
20,047,964
null
The symmetrical arrangement of the histidines in the homodimer of restriction enzyme BfiI poses two problems.
null
109
40,091
0
false
null
null
The symmetrical arrangement of the histidines in the homodimer of restriction enzyme BfiI poses two problems.
true
true
true
true
true
6,919
3
INTRODUCTION
0
null
null
20,047,964
null
First, what are the individual roles of the two identical histidines at the active site?
null
88
40,092
0
false
null
null
First, what are the individual roles of the two identical histidines at the active site?
true
true
true
true
true
6,919
3
INTRODUCTION
0
null
null
20,047,964
null
Does each have a distinct role, or are they interchangeable?
null
60
40,093
0
false
null
null
Does each have a distinct role, or are they interchangeable?
true
true
true
true
true
6,919
3
INTRODUCTION
0
null
null
20,047,964
null
In addition, what contribution, in quantitative terms, does each make to the catalysis of phosphodiester hydrolysis?
null
116
40,094
0
false
null
null
In addition, what contribution, in quantitative terms, does each make to the catalysis of phosphodiester hydrolysis?
true
true
true
true
true
6,919
3
INTRODUCTION
0
null
null
20,047,964
null
Secondly, how does a restriction endonuclease with a single active site cut both DNA strands, despite their opposite (5′–3′ cf.
null
127
40,095
0
false
null
null
Secondly, how does a restriction endonuclease with a single active site cut both DNA strands, despite their opposite (5′–3′ cf.
true
true
true
true
true
6,919
3
INTRODUCTION
0
null
null
20,047,964
null
3′–5′) polarities, to generate a double-strand break.
null
53
40,096
0
false
null
null
3′–5′) polarities, to generate a double-strand break.
false
false
true
true
false
6,919
4
INTRODUCTION
1
9
[ "B9", "B10", "B13", "B16", "B17", "B17" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-15165852|pmid-12470949|pmid-12750473|pmid-12750473|NA
The proposed mechanism for phosphodiester hydrolysis by dimeric PLD enzymes indicates that one of the two active-site histidines in BfiI (H105 from subunit A) should attack the scissile phosphodiester bond to form a covalent intermediate with the 5′-terminal phosphate, while the identical H105 from subunit B protonates...
[ "9", "10", "13", "16", "17", "17" ]
383
40,097
0
false
The proposed mechanism for phosphodiester hydrolysis by dimeric PLD enzymes indicates that one of the two active-site histidines in BfiI should attack the scissile phosphodiester bond to form a covalent intermediate with the 5′-terminal phosphate, while the identical H105 from subunit B protonates the hydroxyl of the 3...
[ "H105 from subunit A", "9,10,13,16" ]
The proposed mechanism for phosphodiester hydrolysis by dimeric PLD enzymes indicates that one of the two active-site histidines in BfiI should attack the scissile phosphodiester bond to form a covalent intermediate with the 5′-terminal phosphate, while the identical H105 from subunit B protonates the hydroxyl of the 3...
true
true
true
true
true
6,920
4
INTRODUCTION
1
9
[ "B9", "B10", "B13", "B16", "B17", "B17" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-15165852|pmid-12470949|pmid-12750473|pmid-12750473|NA
In the second step, the covalent intermediate is hydrolyzed by a water molecule with the aid of H105 from subunit B, which abstracts a proton from the water, to release the cleaved DNA from the enzyme.
[ "9", "10", "13", "16", "17", "17" ]
201
40,098
0
false
In the second step, the covalent intermediate is hydrolyzed by a water molecule with the aid of H105 from subunit B, which abstracts a proton from the water, to release the cleaved DNA from the enzyme.
[]
In the second step, the covalent intermediate is hydrolyzed by a water molecule with the aid of H105 from subunit B, which abstracts a proton from the water, to release the cleaved DNA from the enzyme.
true
true
true
true
true
6,920
4
INTRODUCTION
1
17
[ "B9", "B10", "B13", "B16", "B17", "B17" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-15165852|pmid-12470949|pmid-12750473|pmid-12750473|NA
BfiI acts sequentially on the two DNA strands, to make a double-strand break (17).
[ "9", "10", "13", "16", "17", "17" ]
82
40,099
1
false
BfiI acts sequentially on the two DNA strands, to make a double-strand break.
[ "17" ]
BfiI acts sequentially on the two DNA strands, to make a double-strand break.
true
true
true
true
true
6,920
4
INTRODUCTION
1
9
[ "B9", "B10", "B13", "B16", "B17", "B17" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-15165852|pmid-12470949|pmid-12750473|pmid-12750473|NA
It first cuts the bottom DNA strand 4-nt away from the target site (5′-ACTGGG-3′) and then switches its active site to the top strand before cleaving it 5-nt away.
[ "9", "10", "13", "16", "17", "17" ]
163
40,100
0
false
It first cuts the bottom DNA strand 4-nt away from the target site (5′-ACTGGG-3′) and then switches its active site to the top strand before cleaving it 5-nt away.
[]
It first cuts the bottom DNA strand 4-nt away from the target site (5′-ACTGGG-3′) and then switches its active site to the top strand before cleaving it 5-nt away.
true
true
true
true
true
6,920
4
INTRODUCTION
1
17
[ "B9", "B10", "B13", "B16", "B17", "B17" ]
20,047,964
pmid-17267608|pmid-10074947|pmid-15165852|pmid-12470949|pmid-12750473|pmid-12750473|NA
It was suggested that BfiI uses for the first strand cleavage H105 from one subunit as the nucleophile and the equivalent H105 from the other subunit as the proton donor/acceptor, while the role of each H105 residue is reversed in the cleavage of the complementary strand of opposite polarity (17).
[ "9", "10", "13", "16", "17", "17" ]
298
40,101
1
false
It was suggested that BfiI uses for the first strand cleavage H105 from one subunit as the nucleophile and the equivalent H105 from the other subunit as the proton donor/acceptor, while the role of each H105 residue is reversed in the cleavage of the complementary strand of opposite polarity.
[ "17" ]
It was suggested that BfiI uses for the first strand cleavage H105 from one subunit as the nucleophile and the equivalent H105 from the other subunit as the proton donor/acceptor, while the role of each H105 residue is reversed in the cleavage of the complementary strand of opposite polarity.
true
true
true
true
true
6,920
5
INTRODUCTION
0
null
null
20,047,964
null
In the present study, the mechanism of DNA cleavage by BfiI was elucidated by using heterodimeric variants in which the internal symmetry of its active site was disrupted by substituting one of the two H105 residues in the dimer (Figure 2).
null
240
40,102
0
false
null
null
In the present study, the mechanism of DNA cleavage by BfiI was elucidated by using heterodimeric variants in which the internal symmetry of its active site was disrupted by substituting one of the two H105 residues in the dimer (Figure 2).
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
These variants were then tested against specific oligoduplexes carrying the recognition sequence for BfiI but with either a phosphodiester or a 3′-S-phosphorothiolate (with a bridging 3′-sulfur atom) linkage at the scissile bond.
null
229
40,103
0
false
null
null
These variants were then tested against specific oligoduplexes carrying the recognition sequence for BfiI but with either a phosphodiester or a 3′-S-phosphorothiolate (with a bridging 3′-sulfur atom) linkage at the scissile bond.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
Analysis of the cleavage of these duplexes by WT and by the heterodimeric forms of BfiI allowed us to dissect quantitatively the contribution of the individual histidines to both the formation and the breakdown of the covalent intermediate.
null
240
40,104
0
false
null
null
Analysis of the cleavage of these duplexes by WT and by the heterodimeric forms of BfiI allowed us to dissect quantitatively the contribution of the individual histidines to both the formation and the breakdown of the covalent intermediate.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
Surprisingly, our studies show that BfiI uses the active-site H105 from one particular subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetry related H105 from the opposite subunit acts as the proton donor/acceptor during both strand-sc...
null
334
40,105
0
false
null
null
Surprisingly, our studies show that BfiI uses the active-site H105 from one particular subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetry related H105 from the opposite subunit acts as the proton donor/acceptor during both strand-sc...
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
This represents a novel mechanism for the scission of double-stranded DNA as it requires a single active site to not only switch between strands but also to switch its orientation on the DNA.
null
191
40,106
0
false
null
null
This represents a novel mechanism for the scission of double-stranded DNA as it requires a single active site to not only switch between strands but also to switch its orientation on the DNA.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
Figure 2.Generation of heterodimeric variants of BfiI.
null
54
40,107
0
false
null
null
Figure 2.Generation of heterodimeric variants of BfiI.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
The dimeric forms of His-tagged WT BfiI and the H105A mutant are indicated.
null
75
40,108
0
false
null
null
The dimeric forms of His-tagged WT BfiI and the H105A mutant are indicated.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
In both cases, the BfiI monomer is shown as two domains connected by a linker: a C-terminal DNA-binding domain (shaded diamond) and a N-terminal domain for dimerization and catalysis (unfilled circle); ‘H’ marks H105 in the WT dimer and ‘X’ marks the H105A substitution in the mutant.
null
284
40,109
0
false
null
null
In both cases, the BfiI monomer is shown as two domains connected by a linker: a C-terminal DNA-binding domain (shaded diamond) and a N-terminal domain for dimerization and catalysis (unfilled circle); ‘H’ marks H105 in the WT dimer and ‘X’ marks the H105A substitution in the mutant.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
The His-tagged WT and the H105A homodimers are mixed and completely unfolded with 6 M GdmCl.
null
92
40,110
0
false
null
null
The His-tagged WT and the H105A homodimers are mixed and completely unfolded with 6 M GdmCl.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
Subsequent removal of the denaturant results in formation of three species: the two initial homodimers and the heterodimer.
null
123
40,111
0
false
null
null
Subsequent removal of the denaturant results in formation of three species: the two initial homodimers and the heterodimer.
true
true
true
true
true
6,921
5
INTRODUCTION
0
null
null
20,047,964
null
The heterodimer with a single His-tag is separated from the homodimeric forms of BfiI lacking the His-tag or bearing two His-tags by Ni2+-chelating chromatography.
null
163
40,112
0
false
null
null
The heterodimer with a single His-tag is separated from the homodimeric forms of BfiI lacking the His-tag or bearing two His-tags by Ni2+-chelating chromatography.
true
true
true
true
true
6,921
6
INTRODUCTION
0
null
null
20,047,964
pmid-9689058|pmid-10207000
Generation of heterodimeric variants of BfiI.
null
45
40,113
0
false
null
null
Generation of heterodimeric variants of BfiI.
true
true
true
true
true
6,922
6
INTRODUCTION
0
null
null
20,047,964
pmid-9689058|pmid-10207000
The dimeric forms of His-tagged WT BfiI and the H105A mutant are indicated.
null
75
40,114
0
false
null
null
The dimeric forms of His-tagged WT BfiI and the H105A mutant are indicated.
true
true
true
true
true
6,922
6
INTRODUCTION
0
null
null
20,047,964
pmid-9689058|pmid-10207000
In both cases, the BfiI monomer is shown as two domains connected by a linker: a C-terminal DNA-binding domain (shaded diamond) and a N-terminal domain for dimerization and catalysis (unfilled circle); ‘H’ marks H105 in the WT dimer and ‘X’ marks the H105A substitution in the mutant.
null
284
40,115
0
false
null
null
In both cases, the BfiI monomer is shown as two domains connected by a linker: a C-terminal DNA-binding domain (shaded diamond) and a N-terminal domain for dimerization and catalysis (unfilled circle); ‘H’ marks H105 in the WT dimer and ‘X’ marks the H105A substitution in the mutant.
true
true
true
true
true
6,922