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Q3SMU7

- Q3SMU7_NITWN

UniProt

Q3SMU7 - Q3SMU7_NITWN

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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391)
Status
Unreviewed - 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

Note: Magnesium. 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+) and Ca(2+).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

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA-dependent DNA replication Source: UniProtKB-HAMAP
  2. DNA topological change Source: InterPro
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: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-SubCell
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
Contains Toprim domain.SAAS annotation

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075155.
KOiK02470.
OMAiAFPTHYP.
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.
GeneIDi3676444.
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 .
RefSeqi WP_011313343.1. NC_007406.1.
YP_316624.1. NC_007406.1.

3D structure databases

ProteinModelPortali Q3SMU7.
SMRi Q3SMU7. Positions 25-392.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 323098.Nwi_0004.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABA03272 ; ABA03272 ; Nwi_0004 .
GeneIDi 3676444.
KEGGi nwi:Nwi_0004.
PATRICi 22696297. VBINitWin102302_0005.

Phylogenomic databases

eggNOGi COG0187.
HOGENOMi HOG000075155.
KOi K02470.
OMAi AFPTHYP.
OrthoDBi EOG6P334W.

Enzyme and pathway databases

BioCyci NWIN323098:GJEG-4-MONOMER.

Family and domain databases

Gene3Di 3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPi MF_01898. GyrB.
InterProi 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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view ]
Pfami PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00418. TPI2FAMILY.
SMARTi SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsi TIGR01059. gyrB. 1 hit.
PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: November 26, 2014
This is version 76 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