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P55992

- GYRB_HELPY

UniProt

P55992 - GYRB_HELPY

Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 1 (01 Nov 1997)
      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 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 bindingi422 – 4221Magnesium 1; catalyticUniRule annotation
    Sitei447 – 4471Interaction with DNAUniRule annotation
    Sitei450 – 4501Interaction with DNAUniRule annotation
    Metal bindingi495 – 4951Magnesium 1; catalyticUniRule annotation
    Metal bindingi495 – 4951Magnesium 2UniRule annotation
    Metal bindingi497 – 4971Magnesium 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, Topoisomerase

    Keywords - Ligandi

    ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciHPY:HP0501-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:HP_0501
    OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
    Taxonomic identifieri85962 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
    ProteomesiUP000000429: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. chromosome Source: InterPro
    2. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 773773DNA gyrase subunit BPRO_0000145314Add
    BLAST

    Proteomic databases

    PRIDEiP55992.

    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

    DIPiDIP-3593N.
    IntActiP55992. 3 interactions.
    MINTiMINT-168943.
    STRINGi85962.HP0501.

    Structurei

    3D structure databases

    ProteinModelPortaliP55992.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini416 – 530115ToprimUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0187.
    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.

    P55992-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQNYQSHSIK VLKGLEGVRK RPGMYIGDTN VGGLHHMVYE VVDNAVDESM    50
    AGFCDTINIT LTDEGSCIVE DNGRGIPVDI HPTEKIPACT VVLTILHAGG 100
    KFDNDTYKVS GGLHGVGVSV VNALSKRLIM TIKKEGQIYR QEFEKGIPTS 150
    ELEIIGKTKS AKESGTTIEF FPDESVMEVV EFQAGILQKR FKEMAYLNDG 200
    LKISFKEEKT QLQETYFYED GLKQFVKDSA KKELLTPIIS FKSMDEETRT 250
    SIEVALAYAD DYNENTLSFV NNIKTSEGGT HEAGFKMGLS KAILQYIGNN 300
    IKTKESRPIS EDIKEGLIAV VSLKMSEPLF EGQTKSKLGS SYARALVSKL 350
    VYDKIHQFLE ENPNEAKIIA NKALLAAKAR EASKKARELT RKKDNLSVGT 400
    LPGKLADCQS KDPLESEIFL VEGDSAGGSA KQGRDRVFQA ILPLKGKILN 450
    VEKSHLSKIL KSEEIKNMIT AFGCGIQESF DIERLRYHKI IIMTDADVDG 500
    SHIQTLLMTF FYRYLRPLIE QGHVYIAQAP LYKYKKGKTE IYLKDSVALD 550
    HFLIEHGINS VDIEGIGKND LMNLLKVARH YRYALLELEK RYNLLEILRF 600
    LIETKDALSL DMKVLEKSIL EKLEGLNYQI LRSFATEESL HLHTQTPKGL 650
    VEFNLDDNLF KEVLFEEANY TYQKLMEYNL DFLENKDILA FLEEVENHAK 700
    KGANIQRYKG LGEMNPNDLW ETTMHKENRS LIKLKIEDLE KTDAVFSLCM 750
    GDEVEPRRAF IQAHAKDVKQ LDV 773
    Length:773
    Mass (Da):87,367
    Last modified:November 1, 1997 - v1
    Checksum:iFDB47D3112CE8661
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000511 Genomic DNA. Translation: AAD07566.1.
    PIRiE64582.
    RefSeqiNP_207298.1. NC_000915.1.
    YP_006934423.1. NC_018939.1.

    Genome annotation databases

    EnsemblBacteriaiAAD07566; AAD07566; HP_0501.
    GeneIDi13869691.
    900050.
    KEGGiheo:C694_02575.
    hpy:HP0501.
    PATRICi20592277. VBIHelPyl33062_0527.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000511 Genomic DNA. Translation: AAD07566.1 .
    PIRi E64582.
    RefSeqi NP_207298.1. NC_000915.1.
    YP_006934423.1. NC_018939.1.

    3D structure databases

    ProteinModelPortali P55992.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-3593N.
    IntActi P55992. 3 interactions.
    MINTi MINT-168943.
    STRINGi 85962.HP0501.

    Proteomic databases

    PRIDEi P55992.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD07566 ; AAD07566 ; HP_0501 .
    GeneIDi 13869691.
    900050.
    KEGGi heo:C694_02575.
    hpy:HP0501.
    PATRICi 20592277. VBIHelPyl33062_0527.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci HPY:HP0501-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700392 / 26695.

    Entry informationi

    Entry nameiGYRB_HELPY
    AccessioniPrimary (citable) accession number: P55992
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 95 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Helicobacter pylori
      Helicobacter pylori (strain 26695): entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3