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Protein

DNA gyrase subunit B

Gene

gyrB

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

Functioni

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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca2+.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi439 – 4391Magnesium 1; catalyticUniRule annotation
Sitei464 – 4641Interaction with DNAUniRule annotation
Sitei467 – 4671Interaction with DNAUniRule annotation
Metal bindingi513 – 5131Magnesium 1; catalyticUniRule annotation
Metal bindingi513 – 5131Magnesium 2UniRule annotation
Metal bindingi515 – 5151Magnesium 2UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, TopoisomeraseUniRule annotation

Keywords - Ligandi

ATP-bindingUniRule annotation, DNA-bindingUniRule annotation, MagnesiumUniRule annotation, Metal-bindingUniRule annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciNWIN323098:GJEG-4-MONOMER.

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:Nwi_0004Imported
OrganismiNitrobacter winogradskyi (strain Nb-255 / ATCC 25391)Imported
Taxonomic identifieri323098 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeNitrobacter
ProteomesiUP000002531 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotation

Interactioni

Subunit structurei

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.UniRule annotation

Protein-protein interaction databases

STRINGi323098.Nwi_0004.

Structurei

3D structure databases

ProteinModelPortaliQ3SMU7.
SMRiQ3SMU7. Positions 25-392.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini433 – 548116ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075155.
KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

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.
YP_316624.1. 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.
YP_316624.1. NC_007406.1.

3D structure databases

ProteinModelPortaliQ3SMU7.
SMRiQ3SMU7. Positions 25-392.
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

eggNOGiCOG0187.
HOGENOMiHOG000075155.
KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

Enzyme and pathway databases

BioCyciNWIN323098:GJEG-4-MONOMER.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255."
    Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L., Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J., Hickey W.J.
    Appl. Environ. Microbiol. 72:2050-2063(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Nb-255 / ATCC 25391Imported.

Entry informationi

Entry nameiQ3SMU7_NITWN
AccessioniPrimary (citable) accession number: Q3SMU7
Entry historyi
Integrated into UniProtKB/TrEMBL: October 11, 2005
Last sequence update: October 11, 2005
Last modified: April 29, 2015
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3

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 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.