gyrB:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
ecocyc_update_annotations.php
touch table
 
(31 intermediate revisions by 3 users not shown)
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
DNA gyrase, subunit B<ref name='LIB:Riley_2006'/>, B3699<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NalC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ParA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcbA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcpA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HopA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cou<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HisU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HimB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, GyrB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''DNA gyrase, subunit B<ref name='LIB:Riley_2006'/>, B3699<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NalC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ParA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcbA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PcpA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HopA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Cou<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HisU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, HimB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, GyrB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , acrB, Cou, ECK3691, himB, hisU, hopA, JW5625, nalC, parA, pcbA, pcpA, b3699''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 77: Line 77:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|   id="P46aafc6cd64f9"  class=" tableEdit GO_table_product dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46aafc6cd64f9"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-  
|-  
|
|


|
|
GO:0008094
GO:0003918
|
|
DNA-dependent ATPase activity
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
PMID:6094559
GOA:interpro<br />GO_REF:0000002
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
InterPro:IPR000565
|
|
F
F
|
|
ATPase activity of the GyrB subunit was followed by measuring the release of  32P-labeled phosphate from reactions containing [y-32P]-ATP in the presence of GyrA and DNA (Figure 1). Omission of DNA or GyrA (which binds DNA) resulted in dramatically reduced ATPase activity of GyrB.
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 103: Line 103:


|
|
GO:0003677
GO:0003918
|
|
DNA binding
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
PMID:10764756
GOA:interpro<br />GO_REF:0000002
|
|
IMP: Inferred from Mutant Phenotype
IEA: Inferred from Electronic Annotation
|
|
 
InterPro:IPR001241
|
|
F
F
|
|
A truncated mutant of GyrB that lacks the C-terminal 160 residues has a reduced ability to retard the movement of DNA through a 5% polyacrylamide gel indicating a deficiency in DNA binding (Figure 5).
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 122: Line 122:


|
|
GO:0009330
GO:0003918
|
|
DNA topoisomerase complex (ATP-hydrolyzing)
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
PMID:347446
GOA:interpro<br />GO_REF:0000002
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
InterPro:IPR002288
|
|
C
F
|
|
<i>E. coli</i> gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 141: Line 141:


|
|
GO:0006265
GO:0008094
|
|
DNA topological change
DNA-dependent ATPase activity
|
|
PMID:6327603
PMID:6094559
|
|
IMP: Inferred from Mutant Phenotype
IDA: Inferred from Direct Assay
|
|


|
|
P
F
|
|
Nucleoids from <i>E. coli</i> cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient.  The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2).  The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.
ATPase activity of the GyrB subunit was followed by measuring the release of  32P-labeled phosphate from reactions containing [y-32P]-ATP in the presence of GyrA and DNA (Figure 1).  Omission of DNA or GyrA (which binds DNA) resulted in dramatically reduced ATPase activity of GyrB.
|
|
complete  
complete  
Line 160: Line 160:


|
|
GO:0005524
GO:0003918
|
|
ATP binding
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
PMID:9756859
GOA:interpro<br />GO_REF:0000002
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
InterPro:IPR011557
|
|
F
F
|
|
Using gel filtration and equilibrium ultracentrifugation, the authors showed that the 43kDa N-terminal fragment of GyrB binds to ADPNP, or [32-P]ADPNP, and ATP (Figure 7 and Table 1).
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 179: Line 179:


|
|
GO:0042493
GO:0003918
|
|
response to drug
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
PMID:9144789
GOA:interpro<br />GO_REF:0000002
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
InterPro:IPR013506
|
|
P
F
|
|
Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1.
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 198: Line 198:


|
|
GO:0003918
GO:0003677
|
|
DNA topoisomerase (ATP-hydrolyzing) activity
DNA binding
|
|
PMID:368801
PMID:10764756
|
|
IDA: Inferred from Direct Assay
IMP: Inferred from Mutant Phenotype
|
|


Line 210: Line 210:
F
F
|
|
Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).
A truncated mutant of GyrB that lacks the C-terminal 160 residues has a reduced ability to retard the movement of DNA through a 5% polyacrylamide gel indicating a deficiency in DNA binding (Figure 5).
|
|
complete  
complete  
Line 217: Line 217:


|
|
GO:0003677
GO:0009330
|
|
DNA binding
DNA topoisomerase complex (ATP-hydrolyzing)
|
|
PMID:6294616
PMID:347446
|
|
IDA: Inferred from Direct Assay
IDA: Inferred from Direct Assay
Line 227: Line 227:


|
|
F
C
|
|
E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.
<i>E. coli</i> gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).
|
|
complete  
complete  
Line 236: Line 236:


|
|
GO:0006350
GO:0003918
|
|
transcription<input name="field[2]" type="hidden" value="transcription" />
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
PMID:15535863
GOA:interpro<br />GO_REF:0000002
|
|
IMP: Inferred from Mutant Phenotype
IEA: Inferred from Electronic Annotation
|
|
 
InterPro:IPR013759
|
|
P
F
|
|
The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions.
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 255: Line 255:


|
|
GO:0005737
GO:0006265
|
|
cytoplasm
DNA topological change
|
|
PMID:7952188
PMID:6327603
|
|
IDA: Inferred from Direct Assay
IMP: Inferred from Mutant Phenotype
|
|


|
|
C
P
|
|
Immunogold labeling of cells with anti-GyrB antibodies indicated the presence of GyrB in the cytoplasm of E. coli.
Nucleoids from <i>E. coli</i> cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient.  The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2).  The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.
|
|
complete  
complete  
Line 282: Line 282:
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000565
InterPro:IPR013760
|
|
F
F
Line 288: Line 288:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 301: Line 301:
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001241
InterPro:IPR018522
|
|
F
F
Line 307: Line 307:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|


|
|
GO:0003918
GO:0005524
|
|
DNA topoisomerase (ATP-hydrolyzing) activity
ATP binding
|
|
GOA:interpro<br />GO_REF:0000002
PMID:9756859
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR002288
 
|
|
F
F
|
|
Seeded from [[EcoCyc]] (v14.0)
Using gel filtration and equilibrium ultracentrifugation, the authors showed that the 43kDa N-terminal fragment of GyrB binds to ADPNP, or [32-P]ADPNP, and ATP (Figure 7 and Table 1).
|
|
complete
|-  
|-  
|
|
Line 335: Line 335:
DNA topoisomerase (ATP-hydrolyzing) activity
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
GOA:interpro<br />GO_REF:0000002
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR011557
EC:5.99.1.3
|
|
F
F
Line 345: Line 345:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|


|
|
GO:0003918
GO:0042493
|
|
DNA topoisomerase (ATP-hydrolyzing) activity
response to drug
|
|
GOA:interpro<br />GO_REF:0000002
PMID:9144789
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR013506
 
|
|
F
P
|
|
Seeded from [[EcoCyc]] (v14.0)
Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1.
|
|
complete
|-  
|-  
|
|


|
|
GO:0003918
GO:0005524
|
|
DNA topoisomerase (ATP-hydrolyzing) activity
ATP binding
|
|
GOA:interpro<br />GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
Line 377: Line 377:
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR013759
InterPro:IPR000565
|
|
F
F
Line 383: Line 383:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 392: Line 392:
DNA topoisomerase (ATP-hydrolyzing) activity
DNA topoisomerase (ATP-hydrolyzing) activity
|
|
GOA:interpro<br />GO_REF:0000002
PMID:368801
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR013760
 
|
|
F
F
|
|
Seeded from [[EcoCyc]] (v14.0)
Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).
|
|
complete
|-  
|-  
|
|


|
|
GO:0003918
GO:0003677
|
|
DNA topoisomerase (ATP-hydrolyzing) activity
DNA binding
|
|
GOA:interpro<br />GO_REF:0000002
PMID:6294616
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR018522
 
|
|
F
F
|
|
Seeded from [[EcoCyc]] (v14.0)
E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.
|
|
complete
|-  
|-  
|
|


|
|
GO:0003918
GO:0005524
|
|
DNA topoisomerase (ATP-hydrolyzing) activity
ATP binding
|
|
GOA:spec<br />GO_REF:0000003
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
EC:5.99.1.3
InterPro:IPR001241
|
|
F
F
Line 440: Line 440:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|


|
|
GO:0005524
GO:0006351
|
|
ATP binding
transcription, DNA-dependent
|
|
GOA:interpro<br />GO_REF:0000002
PMID:15535863
|
|
IEA: Inferred from Electronic Annotation
IMP: Inferred from Mutant Phenotype
|
|
InterPro:IPR000565
 
|
|
F
P
|
|
Seeded from [[EcoCyc]] (v14.0)
The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions.
 
GO replaced obsolete GO:0006350
|
|
complete
|-  
|-  
|
|
Line 472: Line 474:
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001241
InterPro:IPR002288
|
|
F
F
Line 478: Line 480:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 491: Line 493:
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR002288
InterPro:IPR003594
|
|
F
F
Line 497: Line 499:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|


|
|
GO:0005524
GO:0005737
|
|
ATP binding
cytoplasm
|
|
GOA:interpro<br />GO_REF:0000002
PMID:7952188
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
InterPro:IPR003594
 
|
|
F
C
|
|
Seeded from [[EcoCyc]] (v14.0)
Immunogold labeling of cells with anti-GyrB antibodies indicated the presence of GyrB in the cytoplasm of E. coli.
|
|
complete
|-  
|-  
|
|
Line 535: Line 537:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 554: Line 556:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 573: Line 575:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 592: Line 594:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 611: Line 613:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 630: Line 632:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 649: Line 651:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 668: Line 670:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 687: Line 689:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 706: Line 708:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 725: Line 727:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 744: Line 746:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 763: Line 765:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 782: Line 784:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 801: Line 803:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 820: Line 822:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 839: Line 841:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 858: Line 860:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 877: Line 879:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 896: Line 898:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 915: Line 917:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 934: Line 936:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 953: Line 955:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 972: Line 974:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 991: Line 993:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 1,010: Line 1,012:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
|-  
|-  
|
|
Line 1,029: Line 1,031:
Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
|
|
complete


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 1,044: Line 1,046:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   id="Y46aafc828890f"  class=" tableEdit Product_interactions_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aafc828890f"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 1,190: Line 1,192:
|
|
Experiment(s):EBI-891214<br />  
Experiment(s):EBI-891214<br />  
|-
|
Protein
|
parE
|


|- class="tableEdit_footer"
|
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table]</span> || || || ||
PMID:19402753
|}
|
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f-->
LCMS(ID Probability):99.6
|-
|
Protein
|
deaD
|


<!--Function_notes--></protect>
|
===Notes===
PMID:19402753
|
MALDI(Z-score):18.677074
|-  
|
Protein
|
metK
|


|
PMID:19402753
|
MALDI(Z-score):33.839565
|-
|
Protein
|
tufB
|


==Localization==
|
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.D46a8886fa565f-->
PMID:19402753
<!--
|
******************************************************************************************
MALDI(Z-score):21.335822
*  
|-
|
Protein
|
gyrA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):28.518798
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table]</span> || || || ||
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.Y46aafc828890f-->
 
<!--Function_notes--></protect>
===Notes===
 
 
==Localization==
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.D46a8886fa565f-->
<!--
******************************************************************************************
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="D46a8886fa565f"  class=" tableEdit Product_localization_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a8886fa565f"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 1,234: Line 1,291:
****************************************************************************************** -->{{Product_physical_properties_help}}
****************************************************************************************** -->{{Product_physical_properties_help}}
{|  id="S46aafc8560656"  class=" tableEdit Product_phys_prop_table"   
{|  id="S46aafc8560656"  class=" tableEdit Product_phys_prop_table"   
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 1,285: Line 1,346:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|   id="A46aafc85dcb1e"  class=" tableEdit Product_motif_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46aafc85dcb1e"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
Line 1,299: Line 1,360:
|
|
   
   
 
|-
|
Domain
|
31..174
|
[http://pfam.janelia.org/family/PF02518 PF02518  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase]
|
 
|
PMID:19920124
|-
|
Domain
|
221..391
|
[http://pfam.janelia.org/family/PF00204 PF00204  DNA gyrase B]
|
 
|
PMID:19920124
|-
|
Domain
|
729..793
|
[http://pfam.janelia.org/family/PF00986 PF00986  DNA gyrase B subunit, carboxyl terminus]
|
 
|
PMID:19920124
 
|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.A46aafc85dcb1e&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.A46aafc85dcb1e&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
Line 1,334: Line 1,428:
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AES6 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AES6 PSI-PRED (P0AES6)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AES6 Genomes TO Protein (P0AES6)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 1,379: Line 1,471:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|   id="F46aafc889e2f8"  class=" tableEdit Product_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46aafc889e2f8"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
 
 
|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table]</span> || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8&page=27976&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.F46aafc889e2f8-->
 
 
<protect><!--Resources_notes--></protect>
<protect><!--Resources_notes--></protect>
===Notes===
===Notes===
 
 
 
 
==Accessions in Other Databases==
==Accessions in Other Databases==
{{BacktoTop}}
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.K46aafc890f82b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.27976.K46aafc890f82b-->
<!--
<!--
******************************************************************************************
******************************************************************************************
*  
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="K46aafc890f82b"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aafc890f82b"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/49176395 GI:49176395]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/YP_026241.1 GeneID:948211]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0012093
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0AES6 UniProtKB/Swiss-Prot:P0AES6]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10424-MONOMER EcoCyc:EG10424-MONOMER]
EcoCyc:EG10424
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AES6 SwissModel:P0AES6]
EcoGene:EG10424
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[[uniprot:P0AES6|UniProt:P0AES6]]
[http://www.ncbi.nlm.nih.gov/gene?term=948211 GeneID:948211]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF02518 PFAM:PF02518]
RegulonDB:ECK120000417
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=YP_026241 RefSeq:YP_026241]
EchoBASE:EB0419
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 1,458: Line 1,578:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="J46a888770be7d"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a888770be7d"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments
Line 1,479: Line 1,599:
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006261_!_DNA-dependent DNA replication]][[Category:GO:0006350_!_transcription]][[Category:Complex:DNA gyrase]][[Category:Products with structures in PDB]]

Latest revision as of 21:07, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

GyrB

Synonyms

DNA gyrase, subunit B[1], B3699[2][1], NalC[2][1], ParA[2][1], PcbA[2][1], PcpA[2][1], HopA[2][1], Cou[2][1], HisU[2][1], HimB[2][1], GyrB[2][1] , acrB, Cou, ECK3691, himB, hisU, hopA, JW5625, nalC, parA, pcbA, pcpA, b3699

Product description

DNA gyrase, subunit B[2][3];

Component of DNA gyrase[3]

DNA gyrase, subunit B; novobiocin, coumermycin resistance[4]

EC number (for enzymes)
edit table


Notes

Function

[back to top]


Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000565

F

Seeded from EcoCyc (v14.0)

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001241

F

Seeded from EcoCyc (v14.0)

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002288

F

Seeded from EcoCyc (v14.0)

complete

GO:0008094

DNA-dependent ATPase activity

PMID:6094559[5]

IDA: Inferred from Direct Assay

F

ATPase activity of the GyrB subunit was followed by measuring the release of 32P-labeled phosphate from reactions containing [y-32P]-ATP in the presence of GyrA and DNA (Figure 1). Omission of DNA or GyrA (which binds DNA) resulted in dramatically reduced ATPase activity of GyrB.

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011557

F

Seeded from EcoCyc (v14.0)

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013506

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

PMID:10764756[6]

IMP: Inferred from Mutant Phenotype

F

A truncated mutant of GyrB that lacks the C-terminal 160 residues has a reduced ability to retard the movement of DNA through a 5% polyacrylamide gel indicating a deficiency in DNA binding (Figure 5).

complete

GO:0009330

DNA topoisomerase complex (ATP-hydrolyzing)

PMID:347446[7]

IDA: Inferred from Direct Assay

C

E. coli gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013759

F

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

PMID:6327603[8]

IMP: Inferred from Mutant Phenotype

P

Nucleoids from E. coli cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient. The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2). The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013760

F

Seeded from EcoCyc (v14.0)

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018522

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

PMID:9756859[9]

IDA: Inferred from Direct Assay

F

Using gel filtration and equilibrium ultracentrifugation, the authors showed that the 43kDa N-terminal fragment of GyrB binds to ADPNP, or [32-P]ADPNP, and ATP (Figure 7 and Table 1).

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.99.1.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0042493

response to drug

PMID:9144789[10]

IDA: Inferred from Direct Assay

P

Coumarin antibiotic sensitivity, including clorobiocin, novobiocin, and coumermycin A1.

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000565

F

Seeded from EcoCyc (v14.0)

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

PMID:368801[11]

IDA: Inferred from Direct Assay

F

Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).

complete

GO:0003677

DNA binding

PMID:6294616[12]

IDA: Inferred from Direct Assay

F

E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001241

F

Seeded from EcoCyc (v14.0)

complete

GO:0006351

transcription, DNA-dependent

PMID:15535863[13]

IMP: Inferred from Mutant Phenotype

P

The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions.

GO replaced obsolete GO:0006350

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002288

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003594

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:7952188[14]

IDA: Inferred from Direct Assay

C

Immunogold labeling of cells with anti-GyrB antibodies indicated the presence of GyrB in the cytoplasm of E. coli.

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011557

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013506

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013759

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013760

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018522

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000565

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001241

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002288

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011557

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013506

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013759

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013760

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:7952188[14]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006261

DNA-dependent DNA replication

PMID:6194415[15]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000565

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001241

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002288

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011557

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013506

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013759

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013760

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018522

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

PMID:6327603[8]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

PMID:15535863[13]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0009330

DNA topoisomerase complex (ATP-hydrolyzing)

PMID:347446[7]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc (v14.0)

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of DNA gyrase

could be indirect

Protein

prsA

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

bglJ

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

deaD

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

glyS

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

gyrA

PMID:15690043[16]

Experiment(s):EBI-884130, EBI-884206, EBI-891214, EBI-891237

Protein

metK

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

rplJ

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

rpsB

PMID:15690043[16]

Experiment(s):EBI-884130

Protein

tufA

PMID:15690043[16]

Experiment(s):EBI-884130, EBI-891214

Protein

yacG

PMID:15690043[16]

Experiment(s):EBI-884130, EBI-879073, EBI-882474, EBI-891214

Protein

parE

PMID:15690043[16]

Experiment(s):EBI-891214

Protein

rplW

PMID:15690043[16]

Experiment(s):EBI-891214

Protein

parE

PMID:19402753[17]

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753[17]

MALDI(Z-score):18.677074

Protein

metK

PMID:19402753[17]

MALDI(Z-score):33.839565

Protein

tufB

PMID:19402753[17]

MALDI(Z-score):21.335822

Protein

gyrA

PMID:19402753[17]

LCMS(ID Probability):99.6 MALDI(Z-score):28.518798

edit table


Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table


Notes

Structure and Physical Properties

[back to top]


Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII
VTIHADNSVS VQDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV
SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT
EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI
FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE
GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLAEY
LLENPTDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL
YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR
DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG
KQEQYIKDDE AMDQYQISIA LDGATLHTNA SAPALAGEAL EKLVSEYNAT QKMINRMERR
YPKAMLKELI YQPTLTEADL SDEQTVTRWV NALVSELNDK EQHGSQWKFD VHTNAEQNLF
EPIVRVRTHG VDTDYPLDHE FITGGEYRRI CTLGEKLRGL LEEDAFIERG ERRQPVASFE
QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL
MGDAVEPRRA FIEENALKAA NIDI
Length

804

Mol. Wt

89.951 kDa

pI

6.0 (calculated)

Extinction coefficient

71,740 - 72,365 (calc based on 26 Y, 6 W, and 5 C residues)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0AES6

Domain

31..174

PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

PMID:19920124[18]

Domain

221..391

PF00204 DNA gyrase B

PMID:19920124[18]

Domain

729..793

PF00986 DNA gyrase B subunit, carboxyl terminus

PMID:19920124[18]

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=gyrB taxon=562,83333 </beststructure>

Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:49176395

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948211

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012093

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AES6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10424

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10424

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948211

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000417

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0419

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]




References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Maxwell, A & Gellert, M (1984) The DNA dependence of the ATPase activity of DNA gyrase. J. Biol. Chem. 259 14472-80 PubMed
  6. ↑ Chatterji, M et al. (2000) The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding. J. Biol. Chem. 275 22888-94 PubMed
  7. ↑ 7.0 7.1 Higgins, NP et al. (1978) Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity. Proc. Natl. Acad. Sci. U.S.A. 75 1773-7 PubMed
  8. ↑ 8.0 8.1 Steck, TR et al. (1984) DNA supercoiling in gyrase mutants. J. Bacteriol. 158 397-403 PubMed
  9. ↑ Kampranis, SC & Maxwell, A (1998) Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase. J. Biol. Chem. 273 26305-9 PubMed
  10. ↑ Tsai, FT et al. (1997) The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins 28 41-52 PubMed
  11. ↑ Sugino, A et al. (1978) Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proc. Natl. Acad. Sci. U.S.A. 75 4838-42 PubMed
  12. ↑ Higgins, NP & Cozzarelli, NR (1982) The binding of gyrase to DNA: analysis by retention by nitrocellulose filters. Nucleic Acids Res. 10 6833-47 PubMed
  13. ↑ 13.0 13.1 Peter, BJ et al. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 5 R87 PubMed
  14. ↑ 14.0 14.1 Thornton, M et al. (1994) Immunogold localization of GyrA and GyrB proteins in Escherichia coli. Microbiology (Reading, Engl.) 140 ( Pt 9) 2371-82 PubMed
  15. ↑ Filutowicz, M & Jonczyk, P (1983) The gyrB gene product functions in both initiation and chain polymerization of Escherichia coli chromosome replication: suppression of the initiation deficiency in gyrB-ts mutants by a class of rpoB mutations. Mol. Gen. Genet. 191 282-7 PubMed
  16. ↑ 16.00 16.01 16.02 16.03 16.04 16.05 16.06 16.07 16.08 16.09 16.10 16.11 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  17. ↑ 17.0 17.1 17.2 17.3 17.4 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  18. ↑ 18.0 18.1 18.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=gyrB:Gene_Product(s)&oldid=1495479"