gyrB:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

gyrB

Gene Synonym(s)

ECK3691, b3699, JW5625, Cou, himB, hisU, nalC, nalD, pcbA, parA, hopA, pcpA[1], acrB, pcpA

Product Desc.

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

Component of DNA gyrase[3]

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

Product Synonyms(s)

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

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): gyrB[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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gyrB is an essential gene.[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

gyrB

Mnemonic

Gyrase

Synonyms

ECK3691, b3699, JW5625, Cou, himB, hisU, nalC, nalD, pcbA, parA, hopA, pcpA[1], acrB, pcpA

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

83.53 minutes, 83.53 minutes 

MG1655: 3878142..3875728
<gbrowseImage> name=NC_000913:3875728..3878142 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3840480..3838066
<gbrowseImage> name=NC_012967:3838066..3840480 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3764061..3766475
<gbrowseImage> name=NC_012759:3764061..3766475 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3760296..3762710
<gbrowseImage> name=NC_007779:3760296..3762710 source=W3110 preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3875731

Edman degradation

PMID:3029692


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

gyrBD426N

D426N

(in nal-24, nal-102, nal-103, nal- 107, nal-108, nal-111, nal-114, en-2 and en-5 mutants; resistant to nalidixic acid and to enoxacin)

Strain variation; seeded from UniProt:P0AES6

gyrBK447E

K447E

(in nal-31, nal-109, nal-115 and nal-120 mutants; resistant to nalidixic acid)

Strain variation; seeded from UniProt:P0AES6

gyrBW751R

W751R

(in B17 resistant mutant)

Strain variation; seeded from UniProt:P0AES6

gyrBSR759RC

SR759RC

(in acriflavine susceptible mutant)

Strain variation; seeded from UniProt:P0AES6

gyrB41(Const)

CGSC:6633

gyrB226

CGSC:5052

gyrB225

CGSC mutation ID:7206

Growth Phenotype

able to grow on beta-glucosides

PMID:6297752

arose as a compensatory mutation in the topA(del) mutant strain DM800

gyrB204

CGSC:9714

gyrB203(ts)

temperature sensitive

CGSC:12298

gyrB221(CouR)

coumermycin resistant

CGSC:12299

gyrB234(ts)

Cell Shape

at permissive temperature (30°C), the average cell volume is larger than the gyrB+ parent (LE234)

PMID:94144

Strain LE316

nalD mutation in strain AB1157-81

Resistant to

Mutant is resistant to Nalidixic acid (NAL)

PMID:3906038

Strain: AB1157-81

Resistance occurs at 37C but sensitive at 30C. Refer to Figure 3 in the Paper for experimental results.

gyrB234(ts)

Resistant to

Resistant to chlorobiocin (50 ug/ml) (at permissive growth temperatures)

PMID:94144

Strain LE316, parental strain LE234

gyrB234(ts)

Growth Phenotype

Temperature-sensitive growth, the plating efficiency at 42°C is less than 10-7 that of the gyrB{ parental strain LE234

PMID:94144

Strain LE316, parental strain is LE234

gyrB234(ts)

Resistant to

Coumermycin A1 resistant (at permissive growth temperatures)

PMID:94144

Strain LE316, parental strain LE234

Multicopy gyrB in strain RYC1010

Resistant to

Increased resistance towards coumermycin A1

PMID:1656457

Plasmid pCID549 was used to increase gene dosage of gyrB causing increased resistance toward coumermycin A1.

gyrB225 (called gyrB-225 in the paper)

6 base pair insertion between nt 1134 and 1135[5]

Insertion of Ala-Arg between residues 378 and 379

Sensitivity to

Increased sensitivity to quinolone

PMID:11399091

Figure 2

quinolones tested: oxolinic acid, CHEBI:138856, ciprofloxacin, CHEBI:100241

experimental Strain: SD104-20

parental strain: SD104


gyrB-225

DNA relaxation

Decreased DNA relaxation by 2 times.

PMID:11399091

See table 1.

gyrB-225

DNA cleavage

DNA cleavage is reduced in mutant. Figure 5.

PMID:11399091

See Figure 5.

gyrB-NI741

Resistant to

Resistant to coumermycin at 60 µg/ml.

PMID:794878

From strain NI708.

Parental strain: K12

gyrB-NI748

Resistant to

Resistant to coumermycin at four times the regular lethal limit (60 µg/ml).

PMID:794878

From strain NI741 and and CRT46 dnaA

Used as a source for drug-resistant DNA gyrase.

gyrB-NT525

Resistant to

Novobiocin at 600 µg/ml.

PMID:794878

Parental strain: K12

Resistance due to drug impermeability.

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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW5625

Plasmid clone

Shigen

PMID:16769691

Status:cloned as old JW

Primer 1:GCCTCGAATTCTTATGACTCCTC

Primer 2:CCAATATCGATATTCGCCGCTTT

3C10

Kohara Phage

Genobase

PMID:3038334

3D1

Kohara Phage

Genobase

PMID:3038334

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[6]

est. P1 cotransduction: 95% [7]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[6]

est. P1 cotransduction: 7% [7]
Synonyms:zie-296::Tn10

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc

EcoCyc:EG10424

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10424

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000417

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948211

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0419

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012093

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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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)
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Notes

Function

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<protect> 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

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

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

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

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

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

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

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

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

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

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

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006261

DNA-dependent DNA replication

PMID:6194415

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

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

PMID:15535863

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0009330

DNA topoisomerase complex (ATP-hydrolyzing)

PMID:347446

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

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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

Experiment(s):EBI-884130

Protein

bglJ

PMID:15690043

Experiment(s):EBI-884130

Protein

deaD

PMID:15690043

Experiment(s):EBI-884130

Protein

glyS

PMID:15690043

Experiment(s):EBI-884130

Protein

gyrA

PMID:15690043

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

Protein

metK

PMID:15690043

Experiment(s):EBI-884130

Protein

rplJ

PMID:15690043

Experiment(s):EBI-884130

Protein

rpsB

PMID:15690043

Experiment(s):EBI-884130

Protein

tufA

PMID:15690043

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

Protein

yacG

PMID:15690043

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

Protein

parE

PMID:15690043

Experiment(s):EBI-891214

Protein

rplW

PMID:15690043

Experiment(s):EBI-891214

Protein

parE

PMID:19402753

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753

MALDI(Z-score):18.677074

Protein

metK

PMID:19402753

MALDI(Z-score):33.839565

Protein

tufB

PMID:19402753

MALDI(Z-score):21.335822

Protein

gyrA

PMID:19402753

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

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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> 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)

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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

Domain

221..391

PF00204 DNA gyrase B

PMID:19920124

Domain

729..793

PF00986 DNA gyrase B subunit, carboxyl terminus

PMID:19920124

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<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:

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</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

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

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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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

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Notes

Links

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Expression

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

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

5.01E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

147.49+/-1.389

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.36174+/-0.03154

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.127381939

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

5582

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1276

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2406

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

gyrB

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Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3878122..3878162 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3699 (EcoliWiki Page)

NCBI GEO profiles for gyrB

microarray

GenExpDB:b3699 (EcoliWiki Page)

Summary of data for gyrB from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (3877671..3877850) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:A11[8]

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Notes

Accessions Related to gyrB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10424

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0419

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3699

EcoGene

EcoGene:EG10424

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000417

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012093

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Shigella flexneri

GYRB

From SHIGELLACYC

E. coli O157

GYRB

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

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

Pfam (EcoliWiki Page)

PF00204 DNA gyrase B

Pfam (EcoliWiki Page)

PF00986 DNA gyrase B subunit, carboxyl terminus

Superfamily (EcoliWiki Page)

SUPERFAMILY:54211

Superfamily (EcoliWiki Page)

SUPERFAMILY:55874

Superfamily (EcoliWiki Page)

SUPERFAMILY:56719

EcoCyc

EcoCyc:EG10424

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10424

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

ASAP

ASAP:ABE-0012093

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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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 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 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 2.11 2.12 2.13 2.14 2.15 2.16 2.17 2.18 2.19 2.20 2.21 2.22 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ McEachern, F & Fisher, LM (1989) Regulation of DNA supercoiling in Escherichia coli: genetic basis of a compensatory mutation in DNA gyrase. FEBS Lett. 253 67-70 PubMed
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  8. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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