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Q839Z1

- Q839Z1_ENTFA

UniProt

Q839Z1 - Q839Z1_ENTFA

Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Unreviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      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 bindingi428 – 4281Magnesium 1; catalyticUniRule annotation
    Sitei453 – 4531Interaction with DNAUniRule annotation
    Sitei456 – 4561Interaction with DNAUniRule annotation
    Metal bindingi501 – 5011Magnesium 1; catalyticUniRule annotation
    Metal bindingi501 – 5011Magnesium 2UniRule annotation
    Metal bindingi503 – 5031Magnesium 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

    BioCyciEFAE226185:GHI1-5-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
    Gene namesi
    Name:gyrBUniRule annotationImported
    Ordered Locus Names:EF_0005Imported
    OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)Imported
    Taxonomic identifieri226185 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
    ProteomesiUP000001415: 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

    STRINGi226185.EF0005.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GEEX-ray1.70A18-224[»]
    4GFNX-ray1.90A18-224[»]
    4GGLX-ray1.69A18-224[»]
    4HXWX-ray1.69A18-224[»]
    4K4OX-ray1.30A18-224[»]
    4KSGX-ray1.75A18-224[»]
    4KSHX-ray1.70A18-224[»]
    4KTNX-ray1.69A18-224[»]
    ProteinModelPortaliQ839Z1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini422 – 536115ToprimUniRule 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

    KOiK02470.
    OMAiEYHRGAP.
    OrthoDBiEOG6P334W.

    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.

    Q839Z1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRERAQEYDA SQIQVLEGLE AVRKRPGMYI GSTSGEGLHH LVWEIVDNSI    50
    DEALAGFAKS IQVIIEPDDS ITVIDDGRGI PVGIQAKTGR PAVETVFTVL 100
    HAGGKFGGGG YKVSGGLHGV GSSVVNALST SLDVRVYKDG KVYYQEYRRG 150
    AVVDDLKVIE ETDRHGTTVH FIPDPEIFTE TTVYDFDKLA TRVRELAFLN 200
    RGLHISIEDR REGQEDKKEY HYEGGIKSYV EHLNANKDVI FPEPIFIEGE 250
    QQDITVEVSM QYTDGYHSNI LSFANNIHTY EGGTHESGFK TSLTRVINDY 300
    ARKQKLMKEN DEKLTGEDVR EGLTAVVSIK HPDPQFEGQT KTKLGNSEVR 350
    TVTDRLFSEY FTKFLMENPT VGKQIVEKGM LASKARLAAK RAREVTRRKG 400
    ALEISNLPGK LADCSSKDPE KCELFIVEGD SAGGSAKQGR SREFQAILPI 450
    RGKILNVEKA SMDKILANEE IRSLFTAMGT GFGEDFDVSK ARYHKLVIMT 500
    DADVDGAHIR TLLLTLFYRF MRPIVEAGYV YIAQPPLYGV KQGKNITYVQ 550
    PGKHAEEELA KVLEELPASP KPSVQRYKGL GEMDDHQLWE TTMDPEKRLM 600
    ARVSVDDAIE ADQIFEMLMG DRVEPRRAFI EENAHYVKNL DI 642
    Length:642
    Mass (Da):71,878
    Last modified:June 1, 2003 - v1
    Checksum:i7A5FD53203C6AEE0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE016830 Genomic DNA. Translation: AAO79890.1.
    RefSeqiNP_813818.1. NC_004668.1.

    Genome annotation databases

    EnsemblBacteriaiAAO79890; AAO79890; EF_0005.
    GeneIDi1198916.
    KEGGiefa:EF0005.
    PATRICi21850447. VBIEntFae7065_0005.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE016830 Genomic DNA. Translation: AAO79890.1 .
    RefSeqi NP_813818.1. NC_004668.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4GEE X-ray 1.70 A 18-224 [» ]
    4GFN X-ray 1.90 A 18-224 [» ]
    4GGL X-ray 1.69 A 18-224 [» ]
    4HXW X-ray 1.69 A 18-224 [» ]
    4K4O X-ray 1.30 A 18-224 [» ]
    4KSG X-ray 1.75 A 18-224 [» ]
    4KSH X-ray 1.70 A 18-224 [» ]
    4KTN X-ray 1.69 A 18-224 [» ]
    ProteinModelPortali Q839Z1.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 226185.EF0005.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAO79890 ; AAO79890 ; EF_0005 .
    GeneIDi 1198916.
    KEGGi efa:EF0005.
    PATRICi 21850447. VBIEntFae7065_0005.

    Phylogenomic databases

    KOi K02470.
    OMAi EYHRGAP.
    OrthoDBi EOG6P334W.

    Enzyme and pathway databases

    BioCyci EFAE226185:GHI1-5-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: ATCC 700802 / V583Imported.
    2. "Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity."
      Tari L.W., Trzoss M., Bensen D.C., Li X., Chen Z., Lam T., Zhang J., Creighton C.J., Cunningham M.L., Kwan B., Stidham M., Shaw K.J., Lightstone F.C., Wong S.E., Nguyen T.B., Nix J., Finn J.
      Bioorg. Med. Chem. Lett. 23:1529-1536(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 18-224.
    3. "A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity."
      Tari L.W., Bensen D.C., Finn J.
      Submitted (APR-2013) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 18-224.
    4. "A new class of type iia topoisomerase inhibitors with broad-spectrum antibacterial activity."
      Tari L.W., Bensen D.C., Finn J.
      Submitted (MAY-2013) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 18-224.
    5. "A new class of type iia topoisomerase inhibitors withbroad-spectrum antibacterial activity."
      Tari L.W., Bensen D.C., Finn J.
      Submitted (MAY-2013) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 18-224.

    Entry informationi

    Entry nameiQ839Z1_ENTFA
    AccessioniPrimary (citable) accession number: Q839Z1
    Entry historyi
    Integrated into UniProtKB/TrEMBL: June 1, 2003
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 98 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiUnreviewed (UniProtKB/TrEMBL)

    Miscellaneousi

    Keywords - Technical termi

    3D-structureImported, Complete proteome, Reference proteomeImported

    External Data

    Dasty 3