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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Staphylococcus aureus (strain N315)
Status
Reviewed-Annotation score: Annotation score: 3 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

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

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

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

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi5.99.1.3. 3352.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:SA0005
OrganismiStaphylococcus aureus (strain N315)
Taxonomic identifieri158879 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus
Proteomesi
  • UP000000751 Componenti: Chromosome

Subcellular locationi

P66937:
  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00001453392 – 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

Structurei

Secondary structure

1644
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
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 strandi501 – 505Combined sources5
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
2XCOX-ray3.10A410-644[»]
2XCQX-ray2.98A410-644[»]
2XCRX-ray3.50B/D/S/U410-644[»]
2XCSX-ray2.10B/D410-543[»]
B/D580-644[»]
2XCTX-ray3.35B/D/S/U410-543[»]
B/D/S/U580-644[»]
4BULX-ray2.60A/C410-543[»]
A/C580-644[»]
5CDMX-ray2.50B/D416-543[»]
B/D580-639[»]
5CDNX-ray2.79B/D/S/U417-543[»]
B/D/S/U580-639[»]
5CDOX-ray3.15B/D/S/U417-543[»]
5CDPX-ray2.45B/D417-543[»]
B/D580-640[»]
5CDQX-ray2.95B/D/S/U414-543[»]
5CDRX-ray2.65B/D417-543[»]
B/D580-640[»]
5NPKX-ray1.98B/D/b/d409-543[»]
B/D/b/d580-642[»]
5NPPX-ray2.22B/D409-543[»]
B/D580-642[»]
ProteinModelPortaliP66937.
SMRiP66937.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP66937.

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

Phylogenomic databases

HOGENOMiHOG000075154.
KOiK02470.
OMAiDCSSRDP.

Family and domain databases

CDDicd00075. HATPase_c. 1 hit.
cd03366. TOPRIM_TopoIIA_GyrB. 1 hit.
Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiView protein in InterPro
IPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR036890. HATPase_C_sf.
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.
IPR034160. TOPRIM_GyrB.
PANTHERiPTHR10169. PTHR10169. 1 hit.
PfamiView protein in Pfam
PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiView protein in PROSITE
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P66937-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVTALSDVNN TDNYGAGQIQ VLEGLEAVRK RPGMYIGSTS ERGLHHLVWE
60 70 80 90 100
IVDNSIDEAL AGYANKIEVV 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:iD4E02886B97DFBC5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000018 Genomic DNA. Translation: BAB41221.1.
PIRiE89758.
RefSeqiWP_000255578.1. NC_002745.2.

Genome annotation databases

EnsemblBacteriaiBAB41221; BAB41221; BAB41221.
KEGGisau:SA0005.

Similar proteinsi

Entry informationi

Entry nameiGYRB_STAAN
AccessioniPrimary (citable) accession number: P66937
Secondary accession number(s): Q99XG6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: January 23, 2007
Last modified: October 25, 2017
This is version 96 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

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