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Q1RHT8

- GYRB_RICBR

UniProt

Q1RHT8 - GYRB_RICBR

Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Rickettsia bellii (strain RML369-C)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 58 (01 Oct 2014)
      Sequence version 1 (16 May 2006)
      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 bindingi435 – 4351Magnesium 1; catalyticUniRule annotation
    Sitei460 – 4601Interaction with DNAUniRule annotation
    Sitei463 – 4631Interaction with DNAUniRule annotation
    Metal bindingi509 – 5091Magnesium 1; catalyticUniRule annotation
    Metal bindingi509 – 5091Magnesium 2UniRule annotation
    Metal bindingi511 – 5111Magnesium 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

    BioCyciRBEL336407:GJCY-1022-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:RBE_0995
    OrganismiRickettsia bellii (strain RML369-C)
    Taxonomic identifieri336407 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiabelli group
    ProteomesiUP000001951: 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 – 808808DNA gyrase subunit BPRO_0000273110Add
    BLAST

    Proteomic databases

    PRIDEiQ1RHT8.

    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

    STRINGi336407.RBE_0995.

    Structurei

    3D structure databases

    ProteinModelPortaliQ1RHT8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini429 – 544116ToprimUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0187.
    HOGENOMiHOG000075155.
    KOiK02470.
    OMAiHIIIMTD.
    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.

    Q1RHT8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSEFEEKLNE SSYGADSIKV LKGLEAVRKR PGMYIGDVGD GSGLHHMIYE    50
    VVDNAIDEAL AGYCDLVRVV LNKNGSVTVS DNGRGIPVEI HEEEGISAAE 100
    VIMTQLHAGG KFDQNSYKVS GGLHGVGVSV VNALSDWLEL RIWRNNTEHL 150
    IRFNNGITEA PLAVVKENVD KKGTEVTFFP SVETFTNIEF DFSIIEHRLR 200
    ELAFLNSGVK ILLTDNRFEE VKEVEFYYTG GIEAYVKYLD RAKHAVHSCI 250
    VVNADNTESG ISLELAMHWN DSYHENILCF TNNIRQRDGG THLSAFKSGL 300
    TRVITAYLEN TGLNKKAKNA FSGEDTREGI CCVLSVKVPD PKFSSQTKDK 350
    LVSSEVRPIV ENAVYTKVLE WFEEHPADAK LIINKIMEAA NAREAARKAR 400
    ELTRRKSVLE VSNLPGKLAD CHAKDPAVSE LFIVEGDSAG GTAKQGRDSK 450
    IQAILPLRGK ILNVERARFD KMLGSDQIGT LITALGTGVD NREFSLEKLR 500
    YHKVIIMTDA DVDGSHIRTL LLTFFYRHMP ELINKGYLYI AQPPLYKVKK 550
    GASELYLKNE QALQDYLVKS AISDATLTLD NKEQLTNENL EELMSKVIKF 600
    NSLLDHASKK FNRSITEILA INDLLNNKIF DNESDSRLKK ALNALNSLEQ 650
    SPDKTDWEVL KHENKIEFFR FSRGLKERKI LLREQLESFE FINISKLALT 700
    IFDVFNKQLK LVVKNQEFDI LTPSILLNTI IECGKKGISV QRFKGLGEMN 750
    SDQLWDTTLD PKKRTLMQVR VAEVDEAEGI FSTLMGDVVE PRRQFIQSNA 800
    LNVVNLDV 808
    Length:808
    Mass (Da):90,843
    Last modified:May 16, 2006 - v1
    Checksum:i9A6B883F87D5D26F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000087 Genomic DNA. Translation: ABE05076.1.
    RefSeqiYP_538165.1. NC_007940.1.

    Genome annotation databases

    EnsemblBacteriaiABE05076; ABE05076; RBE_0995.
    GeneIDi3994964.
    KEGGirbe:RBE_0995.
    PATRICi17883537. VBIRicBel102610_1127.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000087 Genomic DNA. Translation: ABE05076.1 .
    RefSeqi YP_538165.1. NC_007940.1.

    3D structure databases

    ProteinModelPortali Q1RHT8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 336407.RBE_0995.

    Proteomic databases

    PRIDEi Q1RHT8.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABE05076 ; ABE05076 ; RBE_0995 .
    GeneIDi 3994964.
    KEGGi rbe:RBE_0995.
    PATRICi 17883537. VBIRicBel102610_1127.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci RBEL336407:GJCY-1022-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 Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens."
      Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C., Fournier P.-E., Claverie J.-M., Raoult D.
      PLoS Genet. 2:733-744(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: RML369-C.

    Entry informationi

    Entry nameiGYRB_RICBR
    AccessioniPrimary (citable) accession number: Q1RHT8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 23, 2007
    Last sequence update: May 16, 2006
    Last modified: October 1, 2014
    This is version 58 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

    Documents

    1. Rickettsia bellii strain RML369-C
      Rickettsia bellii (strain RML369-C): entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3