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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)DescriptionActionsGraphical viewLength
Metal bindingi435Magnesium 1; catalyticUniRule annotation1
Metal bindingi508Magnesium 1; catalyticUniRule annotation1
Metal bindingi508Magnesium 2UniRule annotation1
Metal bindingi510Magnesium 2UniRule annotation1

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 databases

ChEMBLiCHEMBL1921666.
DrugBankiDB01051. Novobiocin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001453422 – 644DNA gyrase subunit BAdd BLAST643

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)DescriptionActionsGraphical viewLength
Sitei460Interaction with DNAUniRule annotation1
Sitei463Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi93062.SACOL0005.

Chemistry databases

BindingDBiP0A0K8.

Structurei

Secondary structure

1644
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni2 – 4Combined sources3
Helixi17 – 30Combined sources14
Helixi32 – 36Combined sources5
Helixi41 – 60Combined sources20
Beta strandi66 – 72Combined sources7
Helixi73 – 75Combined sources3
Beta strandi76 – 81Combined sources6
Beta strandi89 – 91Combined sources3
Turni92 – 94Combined sources3
Beta strandi95 – 97Combined sources3
Helixi98 – 104Combined sources7
Helixi130 – 133Combined sources4
Beta strandi135 – 144Combined sources10
Beta strandi147 – 154Combined sources8
Beta strandi157 – 160Combined sources4
Beta strandi163 – 167Combined sources5
Beta strandi172 – 179Combined sources8
Turni181 – 183Combined sources3
Helixi192 – 205Combined sources14
Turni206 – 208Combined sources3
Beta strandi210 – 215Combined sources6
Beta strandi223 – 227Combined sources5
Turni426 – 428Combined sources3
Beta strandi430 – 436Combined sources7
Helixi437 – 446Combined sources10
Turni449 – 451Combined sources3
Beta strandi452 – 456Combined sources5
Turni464 – 466Combined sources3
Helixi469 – 473Combined sources5
Helixi476 – 485Combined sources10
Helixi490 – 492Combined sources3
Helixi495 – 497Combined sources3
Beta strandi503 – 505Combined sources3
Helixi511 – 527Combined sources17
Helixi529 – 533Combined sources5
Beta strandi537 – 539Combined sources3
Helixi583 – 585Combined sources3
Helixi588 – 595Combined sources8
Turni598 – 600Combined sources3
Beta strandi604 – 607Combined sources4
Helixi611 – 622Combined sources12
Helixi626 – 636Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5IWIX-ray1.98B/D410-543[»]
B/D580-644[»]
5IWMX-ray2.50B/D410-543[»]
B/D580-644[»]
ProteinModelPortaliP0A0K8.
SMRiP0A0K8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A0K8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini429 – 543ToprimUniRule annotationAdd BLAST115

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. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti40 – 49SERGLHHLVW → QRELHISV in AAA73951 (PubMed:1311298).Curated10
Sequence conflicti66Q → K in AAA73951 (PubMed:1311298).Curated1
Sequence conflicti312 – 321KIMKEEKDRL → RYEEEKIA in AAA73951 (PubMed:1311298).Curated10
Sequence conflicti424K → Q in AAA73951 (PubMed:1311298).Curated1
Sequence conflicti522T → I in AAA73951 (PubMed:1311298).Curated1
Sequence conflicti579R → L in AAA73951 (PubMed:1311298).Curated1

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_MAQU01000005.1.

Genome annotation databases

GeneIDi28379634.

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_MAQU01000005.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5IWIX-ray1.98B/D410-543[»]
B/D580-644[»]
5IWMX-ray2.50B/D410-543[»]
B/D580-644[»]
ProteinModelPortaliP0A0K8.
SMRiP0A0K8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL0005.

Chemistry databases

BindingDBiP0A0K8.
ChEMBLiCHEMBL1921666.
DrugBankiDB01051. Novobiocin.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi28379634.

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. 1 hit.
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...

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: November 2, 2016
This is version 80 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.