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Q3SMU7

- Q3SMU7_NITWN

UniProt

Q3SMU7 - Q3SMU7_NITWN

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
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    • History
      Entry version 74 (01 Oct 2014)
      Sequence version 1 (11 Oct 2005)
      Previous versions | rss
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    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

    Magnesium. 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+ and 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

    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

    Keywords - Molecular functioni

    Isomerase, TopoisomeraseUniRule annotationSAAS annotation

    Keywords - Ligandi

    ATP-bindingUniRule annotationSAAS 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

    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_ATP-bd.
    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

    MNEPARQQIA DTESVAAIEY GAESIRVLKG LDAVRKRPGM YIGDTDDGSG    50
    LHHMVYEVVD NAIDEALAGH ATAVEVILNA DNSVTVRDDG RGIPVDIHKG 100
    EGVSAAEVIM TQLHAGGKFD QNSYKVSGGL HGVGVSVVNA LSSKLTLRIW 150
    RRDKEHLIEF ANGDALAPLK VVGDANGRRG TEVTFLASTE TFTNIEYDFA 200
    TLEHRLRELA FLNSGVNILL SDMRHAVERR EQMMYEGGVV EFVKYLDRNK 250
    KAMVADPIMV RAEMNGISVE AALWWNDSYH ENVLCFTNNI PQRDGGTHLA 300
    GFRGALTRQV NGYADAMAKK ERIALTGDDC REGLTAVLSV KVPDPKFSSQ 350
    TKDKLVSSEV RPVVENVINE ALAAWFEEHP TEAKLIVGKV VEAAAAREAA 400
    RKARELTRRK GALDVASLPG KLADCQERDP AKSELFIVEG DSAGGSAKQG 450
    RNREFQAVLP LRGKILNVER ARFDKMLSSE QIGTLITALG TGIGREDFDL 500
    SKLRYHKIIV MTDADVDGAH IRTLLLTFFF RQMPALIEAG HLYIAQPPLY 550
    KVTRGKSERY LKDERALEDY LIETGLDDCV YKLATGEDRG GRDLLALVDD 600
    ARVIRNVLQN LHGRYNRGVI EQAAIAGVMN PRITENLATA TAAADYIARR 650
    LDALADEVER GWVGRFVEGQ GFFFERTVRG VKDVAMIDDA LLGSADARKL 700
    DEYAGRLQEA YPRPGLLRRR DTETAIHGPV SLFEAVTDAG RKGVALQRYK 750
    GLGEMNPDQL WETTLDVSER SLLQVKIKEV DEADDIFTKL MGDVVEPRRE 800
    FIQDNSLSAN VDV 813
    Length:813
    Mass (Da):89,698
    Last modified:October 11, 2005 - v1
    Checksum:iE2AC610DE795315D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000115 Genomic DNA. Translation: ABA03272.1.
    RefSeqiYP_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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000115 Genomic DNA. Translation: ABA03272.1 .
    RefSeqi 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_ATP-bd.
    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: October 1, 2014
    This is version 74 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