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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 annotationSAAS annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+SAAS annotation
  • Mn2+SAAS annotation

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-bindingSAAS annotation, Isomerase, TopoisomeraseUniRule annotationSAAS annotation
LigandATP-bindingUniRule annotationSAAS annotation, MagnesiumSAAS annotation, Metal-bindingSAAS annotation, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotationSAAS annotation (EC:5.99.1.3UniRule annotationSAAS annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:Nwi_0004Imported
OrganismiNitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255)Imported
Taxonomic identifieri323098 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeNitrobacter
Proteomesi
  • UP000002531 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

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

Protein-protein interaction databases

STRINGi323098.Nwi_0004.

Structurei

3D structure databases

ProteinModelPortaliQ3SMU7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini433 – 548ToprimInterPro annotationAdd BLAST116

Sequence similaritiesi

Belongs to the type II topoisomerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075155.
KOiK02470.
OMAiIKNMITA.
OrthoDBiPOG091H01XP.

Family and domain databases

CDDicd03366. TOPRIM_TopoIIA_GyrB. 1 hit.
Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiView protein in InterPro
IPR002288. 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.
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.
PRINTSiPR00418. TPI2FAMILY.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiView protein in PROSITE
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.

Sequencei

Sequence statusi: Complete.

Q3SMU7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNEPARQQIA DTESVAAIEY GAESIRVLKG LDAVRKRPGM YIGDTDDGSG
60 70 80 90 100
LHHMVYEVVD NAIDEALAGH ATAVEVILNA DNSVTVRDDG RGIPVDIHKG
110 120 130 140 150
EGVSAAEVIM TQLHAGGKFD QNSYKVSGGL HGVGVSVVNA LSSKLTLRIW
160 170 180 190 200
RRDKEHLIEF ANGDALAPLK VVGDANGRRG TEVTFLASTE TFTNIEYDFA
210 220 230 240 250
TLEHRLRELA FLNSGVNILL SDMRHAVERR EQMMYEGGVV EFVKYLDRNK
260 270 280 290 300
KAMVADPIMV RAEMNGISVE AALWWNDSYH ENVLCFTNNI PQRDGGTHLA
310 320 330 340 350
GFRGALTRQV NGYADAMAKK ERIALTGDDC REGLTAVLSV KVPDPKFSSQ
360 370 380 390 400
TKDKLVSSEV RPVVENVINE ALAAWFEEHP TEAKLIVGKV VEAAAAREAA
410 420 430 440 450
RKARELTRRK GALDVASLPG KLADCQERDP AKSELFIVEG DSAGGSAKQG
460 470 480 490 500
RNREFQAVLP LRGKILNVER ARFDKMLSSE QIGTLITALG TGIGREDFDL
510 520 530 540 550
SKLRYHKIIV MTDADVDGAH IRTLLLTFFF RQMPALIEAG HLYIAQPPLY
560 570 580 590 600
KVTRGKSERY LKDERALEDY LIETGLDDCV YKLATGEDRG GRDLLALVDD
610 620 630 640 650
ARVIRNVLQN LHGRYNRGVI EQAAIAGVMN PRITENLATA TAAADYIARR
660 670 680 690 700
LDALADEVER GWVGRFVEGQ GFFFERTVRG VKDVAMIDDA LLGSADARKL
710 720 730 740 750
DEYAGRLQEA YPRPGLLRRR DTETAIHGPV SLFEAVTDAG RKGVALQRYK
760 770 780 790 800
GLGEMNPDQL WETTLDVSER SLLQVKIKEV DEADDIFTKL MGDVVEPRRE
810
FIQDNSLSAN VDV
Length:813
Mass (Da):89,698
Last modified:October 11, 2005 - v1
Checksum:iE2AC610DE795315D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000115 Genomic DNA. Translation: ABA03272.1.
RefSeqiWP_011313343.1. NC_007406.1.

Genome annotation databases

EnsemblBacteriaiABA03272; ABA03272; Nwi_0004.
KEGGinwi:Nwi_0004.
PATRICi22696297. VBINitWin102302_0005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000115 Genomic DNA. Translation: ABA03272.1.
RefSeqiWP_011313343.1. NC_007406.1.

3D structure databases

ProteinModelPortaliQ3SMU7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi323098.Nwi_0004.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA03272; ABA03272; Nwi_0004.
KEGGinwi:Nwi_0004.
PATRICi22696297. VBINitWin102302_0005.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075155.
KOiK02470.
OMAiIKNMITA.
OrthoDBiPOG091H01XP.

Family and domain databases

CDDicd03366. TOPRIM_TopoIIA_GyrB. 1 hit.
Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiView protein in InterPro
IPR002288. 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.
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.
PRINTSiPR00418. TPI2FAMILY.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiView protein in PROSITE
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiQ3SMU7_NITWN
AccessioniPrimary (citable) accession number: Q3SMU7
Entry historyiIntegrated into UniProtKB/TrEMBL: October 11, 2005
Last sequence update: October 11, 2005
Last modified: March 15, 2017
This is version 96 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

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

Complete proteome, Reference proteomeImported

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.