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D7CPP1

- D7CPP1_SYNLT

UniProt

D7CPP1 - D7CPP1_SYNLT

Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Syntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)
Status
Unreviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 34 (01 Oct 2014)
      Sequence version 1 (10 Aug 2010)
      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 bindingi427 – 4271Magnesium 1; catalyticUniRule annotation
    Sitei452 – 4521Interaction with DNAUniRule annotation
    Sitei455 – 4551Interaction with DNAUniRule annotation
    Metal bindingi500 – 5001Magnesium 1; catalyticUniRule annotation
    Metal bindingi500 – 5001Magnesium 2UniRule annotation
    Metal bindingi502 – 5021Magnesium 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

    BioCyciSLIP643648:GHUR-5-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:Slip_0005Imported
    OrganismiSyntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)Imported
    Taxonomic identifieri643648 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesSyntrophomonadaceaeSyntrophothermus
    ProteomesiUP000000378: 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

    Structurei

    3D structure databases

    ProteinModelPortaliD7CPP1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini421 – 535115ToprimUniRule 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

    HOGENOMiHOG000075154.
    KOiK02470.
    OMAiHIIIMTD.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.30.565.10. 1 hit.
    3.40.50.670. 1 hit.
    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. 1 hit.
    TIGRFAMsiTIGR01059. gyrB. 1 hit.
    PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    D7CPP1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNINGSKNEY TALDIQVLEG LEAVRKRPGM YIGSTDSRGL HHLVFEIVDN    50
    SIDEAVAGYC DEIKVIILDD STVTVTDNGR GIPVDMHPKM GIPALEVILT 100
    TLHSGAKFGG SGYTISGGLH GVGLSVVNAL SRWLEVEVAR DGQLYHQRYE 150
    RGKPVTPLAV TGACQTTGTK ITFSPDPEIF EEICFSAEII GQRLRELSYL 200
    NQGTRIVLCD KRTGRDVEYY HTGGIRDFVK YLSKNREPLS PEPIYFRIGK 250
    EGTVVEVAIQ YNTGYTETLL SYANNIHTQE GGTHELGFKN GLTRVVNEYA 300
    KKQGMLKENE GNLLGEDIRE GMTAVISVLV QDPQFEGQTK TKLGNAFIRS 350
    LVEGAVSDFV GAFFDENPSL AKKIVEKAIA ARRAREAARK ARELTRRKNL 400
    LDSTSLPGKL ADCSEKDPAL SELYLVEGDS AGGSAKQGRD RNFQAILPLR 450
    GKILNVEKAR LDKVLSNEEI RALITAIGTG IGEDFDINKA RYHRLIIMTD 500
    ADVDGSHIRV LLLTFFYRYM RPLIEAGYVY VAQPPLYELK RGKEVHYIYN 550
    DRELQRFLEQ QGNKKYGVKR YKGLGEMNPE QLWETTMNPE NRTLLQVRIE 600
    DAIAADVIFS SLMGEKVEPR REFIQENARL VTNLDI 636
    Length:636
    Mass (Da):71,076
    Last modified:August 10, 2010 - v1
    Checksum:i0799A7E8050557BF
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP002048 Genomic DNA. Translation: ADI00813.1.
    RefSeqiWP_013174217.1. NC_014220.1.
    YP_003701378.1. NC_014220.1.

    Genome annotation databases

    EnsemblBacteriaiADI00813; ADI00813; Slip_0005.
    GeneIDi9272772.
    KEGGislp:Slip_0005.
    PATRICi38266332. VBISynLip21176_0006.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP002048 Genomic DNA. Translation: ADI00813.1 .
    RefSeqi WP_013174217.1. NC_014220.1.
    YP_003701378.1. NC_014220.1.

    3D structure databases

    ProteinModelPortali D7CPP1.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ADI00813 ; ADI00813 ; Slip_0005 .
    GeneIDi 9272772.
    KEGGi slp:Slip_0005.
    PATRICi 38266332. VBISynLip21176_0006.

    Phylogenomic databases

    HOGENOMi HOG000075154.
    KOi K02470.
    OMAi HIIIMTD.

    Enzyme and pathway databases

    BioCyci SLIP643648:GHUR-5-MONOMER.

    Family and domain databases

    Gene3Di 3.30.230.10. 1 hit.
    3.30.565.10. 1 hit.
    3.40.50.670. 1 hit.
    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. 1 hit.
    TIGRFAMsi TIGR01059. gyrB. 1 hit.
    PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: DSM 12680 / TGB-C1Imported.

    Entry informationi

    Entry nameiD7CPP1_SYNLT
    AccessioniPrimary (citable) accession number: D7CPP1
    Entry historyi
    Integrated into UniProtKB/TrEMBL: August 10, 2010
    Last sequence update: August 10, 2010
    Last modified: October 1, 2014
    This is version 34 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