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P0AES6 (GYRB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA gyrase subunit B

EC=5.99.1.3
Gene names
Name:gyrB
Synonyms:acrB, himB, hisU, nalC, parA, pcbA
Ordered Locus Names:b3699, JW5625
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length804 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Ref.13 Ref.14 Ref.15

Catalytic activity

ATP-dependent breakage, passage and rejoining of double-stranded DNA. Ref.13 Ref.14 Ref.15 Ref.16

Cofactor

Magnesium. Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ and Ca2+. Ref.13 Ref.14

Enzyme regulation

Target of two classes of inhibitors, coumarins and quinolones. Coumarins bind to GyrB and are competitive inhibitors with respect to ATP. Quinolones bind DNA gyrase when the enzyme is complexed with DNA and trap the enzyme in a covalent reaction intermediate with DNA. HAMAP-Rule MF_01898

Subunit structure

Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis. Ref.13 Ref.14 Ref.15

Subcellular location

Cytoplasm Potential HAMAP-Rule MF_01898.

Sequence similarities

Belongs to the type II topoisomerase family.

Contains 1 Toprim domain.

Ontologies

Keywords
   Biological processAntibiotic resistance
   Cellular componentCytoplasm
   LigandATP-binding
DNA-binding
Magnesium
Metal-binding
Nucleotide-binding
   Molecular functionIsomerase
Topoisomerase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processATP catabolic process

Inferred from direct assay PubMed 368801PubMed 6094559. Source: GOC

DNA topological change

Inferred from mutant phenotype PubMed 6327603. Source: EcoliWiki

DNA-dependent DNA replication

Inferred from Biological aspect of Ancestor. Source: RefGenome

chromosome segregation

Inferred from Biological aspect of Ancestor. Source: RefGenome

response to antibiotic

Inferred from electronic annotation. Source: UniProtKB-KW

response to drug

Inferred from direct assay PubMed 9144789. Source: EcoliWiki

transcription, DNA-templated

Inferred from mutant phenotype PubMed 15535863. Source: EcoliWiki

   Cellular_componentDNA topoisomerase complex (ATP-hydrolyzing)

Inferred from direct assay PubMed 347446. Source: EcoliWiki

chromosome

Inferred from electronic annotation. Source: InterPro

cytoplasm

Inferred from direct assay PubMed 7952188. Source: EcoliWiki

nucleoid

Inferred from Biological aspect of Ancestor. Source: RefGenome

   Molecular_functionATP binding

Inferred from direct assay PubMed 9756859. Source: EcoliWiki

DNA binding

Inferred from direct assay PubMed 6294616. Source: EcoliWiki

DNA topoisomerase type II (ATP-hydrolyzing) activity

Inferred from direct assay PubMed 368801. Source: EcoliWiki

DNA-dependent ATPase activity

Inferred from direct assay PubMed 6094559. Source: EcoliWiki

magnesium ion binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

protein binding

Inferred from physical interaction PubMed 15690043. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

gyrAP0AES45EBI-541911,EBI-547129

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed HAMAP-Rule MF_01898
Chain2 – 804803DNA gyrase subunit B HAMAP-Rule MF_01898
PRO_0000145309

Regions

Domain418 – 533116Toprim

Sites

Metal binding4241Magnesium 1; catalytic By similarity
Metal binding4981Magnesium 1; catalytic By similarity
Metal binding4981Magnesium 2 By similarity
Metal binding5001Magnesium 2 By similarity
Site4491Interaction with DNA By similarity
Site4521Interaction with DNA By similarity

Natural variations

Natural variant4261D → N 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.
Natural variant4471K → E in nal-31, nal-109, nal-115 and nal-120 mutants; resistant to nalidixic acid.
Natural variant7511W → R in B17 resistant mutant.
Natural variant759 – 7602SR → RC in acriflavine susceptible mutant.

Experimental info

Mutagenesis4241E → A or Q: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13
Mutagenesis4981D → A or N: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13
Mutagenesis5001D → A: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13
Mutagenesis5021D → A: Strongly reduced activity regarding both DNA supercoiling and relaxation. Reduces ATP hydrolysis in response to DNA binding, but has only minor effect on the basal rate of ATP hydrolysis. Ref.13
Sequence conflict3851A → P in AAA62050. Ref.4
Sequence conflict4361R → G in BAA20341. Ref.3

Secondary structure

....................................................................................................................................... 804
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AES6 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: D831B95FFB3A7EE3

FASTA80489,950
        10         20         30         40         50         60 
MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII 

        70         80         90        100        110        120 
VTIHADNSVS VQDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV 

       130        140        150        160        170        180 
SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT 

       190        200        210        220        230        240 
EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI 

       250        260        270        280        290        300 
FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE 

       310        320        330        340        350        360 
GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLAEY 

       370        380        390        400        410        420 
LLENPTDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL 

       430        440        450        460        470        480 
YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR 

       490        500        510        520        530        540 
DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG 

       550        560        570        580        590        600 
KQEQYIKDDE AMDQYQISIA LDGATLHTNA SAPALAGEAL EKLVSEYNAT QKMINRMERR 

       610        620        630        640        650        660 
YPKAMLKELI YQPTLTEADL SDEQTVTRWV NALVSELNDK EQHGSQWKFD VHTNAEQNLF 

       670        680        690        700        710        720 
EPIVRVRTHG VDTDYPLDHE FITGGEYRRI CTLGEKLRGL LEEDAFIERG ERRQPVASFE 

       730        740        750        760        770        780 
QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL 

       790        800 
MGDAVEPRRA FIEENALKAA NIDI 

« Hide

References

« Hide 'large scale' references
[1]"Nalidixic acid-resistant mutations of the gyrB gene of Escherichia coli."
Yamagishi J., Yoshida H., Yamayoshi M., Nakamura S.
Mol. Gen. Genet. 204:367-373(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy."
Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H., Gellert M., Mizuuchi K.
Nucleic Acids Res. 15:771-784(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[3]"acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase."
Funatsuki K., Tanaka R., Inagaki S., Konno H., Katoh K., Nakamura H.
J. Biol. Chem. 272:13302-13308(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12 / N2879.
[4]"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[6]"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005."
Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L.
Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION TO 385.
[7]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]"DNA sequence and transcription of the region upstream of the E. coli gyrB gene."
Adachi T., Mizuuchi K., Menzel R., Gellert M.
Nucleic Acids Res. 12:6389-6395(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-106.
Strain: K12.
[9]"Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment."
Menzel R., Gellert M.
J. Bacteriol. 169:1272-1278(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
[10]"Characterization of the ATP binding site on Escherichia coli DNA gyrase. Affinity labeling of Lys-103 and Lys-110 of the B subunit by pyridoxal 5'-diphospho-5'-adenosine."
Tamura J.K., Gellert M.
J. Biol. Chem. 265:21342-21349(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 93-129.
[11]"The peptide antibiotic microcin B17 induces double-strand cleavage of DNA mediated by E. coli DNA gyrase."
Vizan J.L., Hernandez-Chico C., del Castillo I., Moreno F.
EMBO J. 10:467-476(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANTS B17 RESISTANT.
[12]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[13]"The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism."
Noble C.G., Maxwell A.
J. Mol. Biol. 318:361-371(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, MUTAGENESIS OF GLU-424; ASP-498; ASP-500 AND ASP-502.
[14]"DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action."
Sissi C., Chemello A., Vazquez E., Mitchenall L.A., Maxwell A., Palumbo M.
Biochemistry 47:8538-8545(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT.
[15]"A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function."
Schoeffler A.J., May A.P., Berger J.M.
Nucleic Acids Res. 38:7830-7844(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 388-804, SUBUNIT, CATALYTIC ACTIVITY, FUNCTION.
[16]"Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors."
Brvar M., Perdih A., Renko M., Anderluh G., Turk D., Solmajer T.
J. Med. Chem. 55:6413-6426(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 1-220, CATALYTIC ACTIVITY.
[17]"Quinolone resistance-determining region in the DNA gyrase gyrB gene of Escherichia coli."
Yoshida H., Bogaki M., Nakamura M., Yamanaka L.M., Nakamura S.
Antimicrob. Agents Chemother. 35:1647-1650(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS QUINOLONE-RESISTANT.
Strain: K16.
[18]"Crystal structure of an N-terminal fragment of the DNA gyrase B protein."
Wigley D.B., Davies G.J., Dodson E.J., Maxwell A., Dodson G.
Nature 351:624-629(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-393.
[19]"The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study."
Holdgate G.A., Tunnicliffe A., Ward W.H., Weston S.A., Rosenbrock G., Barth P.T., Taylor I.W., Pauptit R.A., Timms D.
Biochemistry 36:9663-9673(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-221 OF MUTANT HIS-136.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X04341 Genomic DNA. Translation: CAA27871.1.
D87842 Genomic DNA. Translation: BAA20341.1.
L10328 Genomic DNA. Translation: AAA62050.1.
U00096 Genomic DNA. Translation: AAT48201.1.
AP009048 Genomic DNA. Translation: BAE77595.1.
M15548 Genomic DNA. Translation: AAA23949.1.
PIRISECTB. D65172.
RefSeqYP_026241.1. NC_000913.3.
YP_491736.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AJ6X-ray2.30A2-220[»]
1EI1X-ray2.30A/B6-392[»]
1KZNX-ray2.30A15-219[»]
3G7EX-ray2.20A15-217[»]
3NUHX-ray3.10B389-804[»]
4DUHX-ray1.50A/B1-220[»]
4HYPX-ray2.60A/B/C/D15-220[»]
4KFGX-ray1.60A/B15-220[»]
ProteinModelPortalP0AES6.
SMRP0AES6. Positions 10-392, 402-784.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-48005N.
IntActP0AES6. 18 interactions.
STRING511145.b3699.

Chemistry

BindingDBP0AES6.
ChEMBLCHEMBL2311224.
DrugBankDB00817. Rosoxacin.

Proteomic databases

PaxDbP0AES6.
PRIDEP0AES6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAT48201; AAT48201; b3699.
BAE77595; BAE77595; BAE77595.
GeneID12930543.
948211.
KEGGecj:Y75_p3474.
eco:b3699.
PATRIC32122895. VBIEscCol129921_3823.

Organism-specific databases

EchoBASEEB0419.
EcoGeneEG10424. gyrB.

Phylogenomic databases

eggNOGCOG0187.
HOGENOMHOG000075155.
KOK02470.
OMAHIIIMTD.
OrthoDBEOG6P334W.
PhylomeDBP0AES6.

Enzyme and pathway databases

BioCycEcoCyc:EG10424-MONOMER.
ECOL316407:JW5625-MONOMER.
MetaCyc:EG10424-MONOMER.

Gene expression databases

GenevestigatorP0AES6.

Family and domain databases

Gene3D3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPMF_01898. GyrB.
InterProIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00418. TPI2FAMILY.
SMARTSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsTIGR01059. gyrB. 1 hit.
PROSITEPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0AES6.
PROP0AES6.

Entry information

Entry nameGYRB_ECOLI
AccessionPrimary (citable) accession number: P0AES6
Secondary accession number(s): O08438, P06982, Q2M811
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene