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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Staphylococcus aureus
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.UniRule annotation

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: 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+ or Ca2+.UniRule annotation

Enzyme regulationi

Pyrazolthiazoles inhibit the ATPase activity of GyrB (PubMed:20356737).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi435 – 4351Magnesium 1; catalyticUniRule annotation
Metal bindingi508 – 5081Magnesium 1; catalyticUniRule annotation
Metal bindingi508 – 5081Magnesium 2UniRule annotation
Metal bindingi510 – 5101Magnesium 2UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
OrganismiStaphylococcus aureus
Taxonomic identifieri1280 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL3038482.
DrugBankiDB01051. Novobiocin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 644643DNA gyrase subunit BPRO_0000145342Add
BLAST

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei460 – 4601Interaction with DNAUniRule annotation
Sitei463 – 4631Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi93062.SACOL0005.

Chemistry

BindingDBiP0A0K8.

Structurei

Secondary structure

1
644
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni2 – 43Combined sources
Helixi17 – 3014Combined sources
Helixi32 – 365Combined sources
Helixi41 – 6020Combined sources
Beta strandi66 – 727Combined sources
Helixi73 – 753Combined sources
Beta strandi76 – 816Combined sources
Beta strandi89 – 913Combined sources
Turni92 – 943Combined sources
Beta strandi95 – 973Combined sources
Helixi98 – 1047Combined sources
Helixi130 – 1334Combined sources
Beta strandi135 – 14410Combined sources
Beta strandi147 – 1548Combined sources
Beta strandi157 – 1604Combined sources
Beta strandi163 – 1675Combined sources
Beta strandi172 – 1798Combined sources
Turni181 – 1833Combined sources
Helixi192 – 20514Combined sources
Turni206 – 2083Combined sources
Beta strandi210 – 2156Combined sources
Beta strandi223 – 2275Combined sources
Turni426 – 4283Combined sources
Beta strandi430 – 4367Combined sources
Helixi437 – 44610Combined sources
Turni449 – 4513Combined sources
Beta strandi452 – 4565Combined sources
Turni464 – 4663Combined sources
Helixi469 – 4735Combined sources
Helixi476 – 48510Combined sources
Helixi490 – 4923Combined sources
Helixi495 – 4973Combined sources
Beta strandi503 – 5053Combined sources
Helixi511 – 52717Combined sources
Helixi529 – 5335Combined sources
Beta strandi537 – 5393Combined sources
Helixi583 – 5853Combined sources
Helixi588 – 5958Combined sources
Turni598 – 6003Combined sources
Beta strandi604 – 6074Combined sources
Helixi611 – 62212Combined sources
Helixi626 – 63611Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3G75X-ray2.30A/B24-230[»]
3G7BX-ray2.30A/B24-230[»]
3TTZX-ray1.63A/B14-233[»]
3U2DX-ray1.85A/B14-233[»]
3U2KX-ray1.64A/B14-233[»]
4PLBX-ray2.69B/D410-543[»]
B/D580-644[»]
4URMX-ray2.94A/B/C/D1-231[»]
4UROX-ray2.59A/B/C/D1-231[»]
5BS3X-ray2.65B/D410-543[»]
B/D580-644[»]
5CPHX-ray1.20A/B2-234[»]
5CTUX-ray1.45A/B2-234[»]
5CTWX-ray1.48A/B2-234[»]
5CTXX-ray1.60A/B2-234[»]
5CTYX-ray1.60A/B2-234[»]
5D6PX-ray2.05A/B2-234[»]
5D6QX-ray1.50A/B2-234[»]
5D7CX-ray1.55A/B2-234[»]
5D7DX-ray1.60A/B2-234[»]
5D7RX-ray1.55A/B2-234[»]
ProteinModelPortaliP0A0K8.
SMRiP0A0K8. Positions 13-644.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A0K8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini429 – 543115ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A0K8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVTALSDVNN TDNYGAGQIQ VLEGLEAVRK RPGMYIGSTS ERGLHHLVWE
60 70 80 90 100
IVDNSIDEAL AGYANQIEVV IEKDNWIKVT DNGRGIPVDI QEKMGRPAVE
110 120 130 140 150
VILTVLHAGG KFGGGGYKVS GGLHGVGSSV VNALSQDLEV YVHRNETIYH
160 170 180 190 200
QAYKKGVPQF DLKEVGTTDK TGTVIRFKAD GEIFTETTVY NYETLQQRIR
210 220 230 240 250
ELAFLNKGIQ ITLRDERDEE NVREDSYHYE GGIKSYVELL NENKEPIHDE
260 270 280 290 300
PIYIHQSKDD IEVEIAIQYN SGYATNLLTY ANNIHTYEGG THEDGFKRAL
310 320 330 340 350
TRVLNSYGLS SKIMKEEKDR LSGEDTREGM TAIISIKHGD PQFEGQTKTK
360 370 380 390 400
LGNSEVRQVV DKLFSEHFER FLYENPQVAR TVVEKGIMAA RARVAAKKAR
410 420 430 440 450
EVTRRKSALD VASLPGKLAD CSSKSPEECE IFLVEGDSAG GSTKSGRDSR
460 470 480 490 500
TQAILPLRGK ILNVEKARLD RILNNNEIRQ MITAFGTGIG GDFDLAKARY
510 520 530 540 550
HKIVIMTDAD VDGAHIRTLL LTFFYRFMRP LIEAGYVYIA QPPLYKLTQG
560 570 580 590 600
KQKYYVYNDR ELDKLKSELN PTPKWSIARY KGLGEMNADQ LWETTMNPEH
610 620 630 640
RALLQVKLED AIEADQTFEM LMGDVVENRR QFIEDNAVYA NLDF
Length:644
Mass (Da):72,540
Last modified:January 23, 2007 - v2
Checksum:iCED22E8C446A1138
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti40 – 4910SERGLHHLVW → QRELHISV in AAA73951 (PubMed:1311298).Curated
Sequence conflicti66 – 661Q → K in AAA73951 (PubMed:1311298).Curated
Sequence conflicti312 – 32110KIMKEEKDRL → RYEEEKIA in AAA73951 (PubMed:1311298).Curated
Sequence conflicti424 – 4241K → Q in AAA73951 (PubMed:1311298).Curated
Sequence conflicti522 – 5221T → I in AAA73951 (PubMed:1311298).Curated
Sequence conflicti579 – 5791R → L in AAA73951 (PubMed:1311298).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71437 Genomic DNA. Translation: CAA50570.1.
D10489 Genomic DNA. Translation: BAA01369.1.
M86227 Genomic DNA. Translation: AAA73951.1.
M37915 Genomic DNA. Translation: AAA26635.1.
PIRiA40585.
RefSeqiWP_000255586.1. NZ_LOSC01000004.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71437 Genomic DNA. Translation: CAA50570.1.
D10489 Genomic DNA. Translation: BAA01369.1.
M86227 Genomic DNA. Translation: AAA73951.1.
M37915 Genomic DNA. Translation: AAA26635.1.
PIRiA40585.
RefSeqiWP_000255586.1. NZ_LOSC01000004.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3G75X-ray2.30A/B24-230[»]
3G7BX-ray2.30A/B24-230[»]
3TTZX-ray1.63A/B14-233[»]
3U2DX-ray1.85A/B14-233[»]
3U2KX-ray1.64A/B14-233[»]
4PLBX-ray2.69B/D410-543[»]
B/D580-644[»]
4URMX-ray2.94A/B/C/D1-231[»]
4UROX-ray2.59A/B/C/D1-231[»]
5BS3X-ray2.65B/D410-543[»]
B/D580-644[»]
5CPHX-ray1.20A/B2-234[»]
5CTUX-ray1.45A/B2-234[»]
5CTWX-ray1.48A/B2-234[»]
5CTXX-ray1.60A/B2-234[»]
5CTYX-ray1.60A/B2-234[»]
5D6PX-ray2.05A/B2-234[»]
5D6QX-ray1.50A/B2-234[»]
5D7CX-ray1.55A/B2-234[»]
5D7DX-ray1.60A/B2-234[»]
5D7RX-ray1.55A/B2-234[»]
ProteinModelPortaliP0A0K8.
SMRiP0A0K8. Positions 13-644.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL0005.

Chemistry

BindingDBiP0A0K8.
ChEMBLiCHEMBL3038482.
DrugBankiDB01051. Novobiocin.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.

Miscellaneous databases

EvolutionaryTraceiP0A0K8.
PROiP0A0K8.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Cloning, sequencing, and expression of the DNA gyrase genes from Staphylococcus aureus."
    Brockbank S.M.V., Barth P.T.
    J. Bacteriol. 175:3269-3277(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-27 AND 314-335.
    Strain: 601055.
  2. "Quinolone resistance mutations in the DNA gyrase gyrA and gyrB genes of Staphylococcus aureus."
    Ito H., Yoshida H., Bogaki-Shonai M., Niga T., Hattori H., Nakamura S.
    Antimicrob. Agents Chemother. 38:2014-2023(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 12600 / IAM 12544 / NCTC 8532.
  3. "Nucleotide sequence of the Staphylococcus aureus gyrB-gyrA locus encoding the DNA gyrase A and B proteins."
    Margerrison E.E.C., Hopewell R., Fisher L.M.
    J. Bacteriol. 174:1596-1603(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "Nucleotide sequence of the recF gene cluster from Staphylococcus aureus and complementation analysis in Bacillus subtilis recF mutants."
    Alonso J.C., Fisher L.M.
    Mol. Gen. Genet. 246:680-686(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-30.
    Strain: YB886.
  5. "DNA cloning and organization of the Staphylococcus aureus gyrA and gyrB genes: close homology among gyrase proteins and implications for 4-quinolone action and resistance."
    Hopewell R., Oram M., Briesewitz R., Fisher L.M.
    J. Bacteriol. 172:3481-3484(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 593-644.
  6. Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 24-230 IN COMPLEX WITH PYRAZOLTHIAZOLE INHIBITOR, ENZYME REGULATION.

Entry informationi

Entry nameiGYRB_STAAU
AccessioniPrimary (citable) accession number: P0A0K8
Secondary accession number(s): P20832
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 77 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.UniRule annotation

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.