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B8EMQ0

- B8EMQ0_METSB

UniProt

B8EMQ0 - B8EMQ0_METSB

Protein

DNA topoisomerase 1

Gene

topA

Organism
Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
Status
Unreviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 47 (01 Oct 2014)
      Sequence version 1 (03 Mar 2009)
      Previous versions | rss
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    Functioni

    Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.UniRule annotationSAAS annotation

    Catalytic activityi

    ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotationSAAS annotation

    Cofactori

    Magnesium. Binds two Mg2+ per subunit.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi7 – 71Magnesium 1; catalyticUniRule annotation
    Sitei31 – 311Interaction with DNAUniRule annotation
    Metal bindingi80 – 801Magnesium 1; catalyticUniRule annotation
    Metal bindingi80 – 801Magnesium 2UniRule annotation
    Metal bindingi82 – 821Magnesium 2UniRule annotation
    Sitei141 – 1411Interaction with DNAUniRule annotation
    Sitei142 – 1421Interaction with DNAUniRule annotation
    Sitei145 – 1451Interaction with DNAUniRule annotation
    Sitei157 – 1571Interaction with DNAUniRule annotation
    Active sitei303 – 3031O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei305 – 3051Interaction with DNAUniRule annotation
    Sitei500 – 5001Interaction with DNAUniRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: UniProtKB-KW
    3. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
    4. magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. DNA topological change Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase, TopoisomeraseUniRule annotationSAAS annotation

    Keywords - Ligandi

    DNA-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation

    Enzyme and pathway databases

    BioCyciMSIL395965:GCND-3902-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
    Alternative name(s):
    DNA topoisomerase IUniRule annotation
    Gene namesi
    Name:topAUniRule annotation
    Ordered Locus Names:Msil_3847Imported
    OrganismiMethylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)Imported
    Taxonomic identifieri395965 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMethylocella
    ProteomesiUP000002257: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    STRINGi395965.Msil_3847.

    Structurei

    3D structure databases

    ProteinModelPortaliB8EMQ0.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 117117ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni165 – 1706Interaction with DNAUniRule annotation

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG1754.
    HOGENOMiHOG000004020.
    KOiK03168.
    OMAiFRSAEYW.
    OrthoDBiEOG6S7XQ9.

    Family and domain databases

    Gene3Di1.10.460.10. 2 hits.
    2.70.20.10. 2 hits.
    3.40.50.140. 1 hit.
    HAMAPiMF_00952. Topoisom_1_prok.
    InterProiIPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR023406. Topo_IA_AS.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013825. Topo_IA_cen_sub2.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR013498. Topo_IA_Znf.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR025589. Toprim_C_rpt.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF13368. Toprim_C_rpt. 4 hits.
    PF01396. zf-C4_Topoisom. 1 hit.
    [Graphical view]
    PRINTSiPR00417. PRTPISMRASEI.
    SMARTiSM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view]
    SUPFAMiSSF56712. SSF56712. 2 hits.
    TIGRFAMsiTIGR01051. topA_bact. 1 hit.
    PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    B8EMQ0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MYVVIVESPA KAKSINKYLG KGYEVYPSYG HVRDLPAKDG SVDPDADFAM    50
    LWDVDVKSAK RLNEIARAVK DADKIILATD PDREGEAISW HVLEVLKAKK 100
    VLKDKPVERV VFNAITKSAV LEAMQHPRQI DVALVDAYLA RRALDYLVGF 150
    NLSPVLWRKL PGARSAGRVQ SVALRLVCDR ELEIEAFVAR EYWSIVAHLR 200
    TQADAPFTAR LVGADGKKIT RLDVGTGAEA AAFKTDLENA TFRVAEIEAK 250
    PAKRHPSAPF TTSTLQQEAS RKLGFAPART MQLAQRLYEG ADIDGETVGL 300
    ITYMRTDGVD LAPEAITSAR SVIARQFGDA YVPKAPRKYT VKAKNAQEAH 350
    EAIRPTDLAR LPRAVARALE PDQAKLYELI WTRTIASQME SAELERTTVD 400
    IEALAGARKL DLRATGQVVR FDGFLKLYQE GRDDEDDDES ARLPDMAKDE 450
    RLKRERIEAD QHFTEPPPRF TEATLVKRME ELGIGRPSTY ASTLAVLRER 500
    DYVRIEKKRL HPEDKGRLVT AFLEAFFARY VGYDFTADLE EKLDRVSNHE 550
    IDWKQVLRDF WLDFSGALAG TKDLRTTEVL DRLNEILGPH IFPPKEDGSD 600
    PRGCPSCGEG KLSLKLGKFG AFIGCSNYPE CKFTRTLAAP DGAEANGGER 650
    PGVKSLGVDP DSGEEITLRD GRFGVYVQQG EGEKPKRSSL PPTIAPADLT 700
    LEQAIALLSL PREVARHPES KEPIVAGIGR YGPYVQHGKT YANVAKDEDI 750
    ISIGANRAID LIVAKESGLT GRRFGASESA PARVLGEHPA GGAVSVKAGR 800
    YGPYVTHGKI NATLPKEADP TTLTLEGAVA LLAAKASGGG APMQGRLLGD 850
    HPSGGPITVR AGRFGAYVNH GKTNATLKRD ASAETITLEE AIRLIEDKEA 900
    AGGGPRKAAA PKKAAKSSAA AKKAAPNAKN KTAPANDEDP PFEPSPNRKP 950
    AAKAAAAAHK KPAAKAAAAK LKQAKQA 977
    Length:977
    Mass (Da):106,066
    Last modified:March 3, 2009 - v1
    Checksum:iD99B73E5B0748473
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001280 Genomic DNA. Translation: ACK52729.1.
    RefSeqiYP_002364091.1. NC_011666.1.

    Genome annotation databases

    EnsemblBacteriaiACK52729; ACK52729; Msil_3847.
    GeneIDi7092543.
    KEGGimsl:Msil_3847.
    PATRICi22603546. VBIMetSil55537_4120.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001280 Genomic DNA. Translation: ACK52729.1 .
    RefSeqi YP_002364091.1. NC_011666.1.

    3D structure databases

    ProteinModelPortali B8EMQ0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 395965.Msil_3847.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACK52729 ; ACK52729 ; Msil_3847 .
    GeneIDi 7092543.
    KEGGi msl:Msil_3847.
    PATRICi 22603546. VBIMetSil55537_4120.

    Phylogenomic databases

    eggNOGi COG1754.
    HOGENOMi HOG000004020.
    KOi K03168.
    OMAi FRSAEYW.
    OrthoDBi EOG6S7XQ9.

    Enzyme and pathway databases

    BioCyci MSIL395965:GCND-3902-MONOMER.

    Family and domain databases

    Gene3Di 1.10.460.10. 2 hits.
    2.70.20.10. 2 hits.
    3.40.50.140. 1 hit.
    HAMAPi MF_00952. Topoisom_1_prok.
    InterProi IPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR023406. Topo_IA_AS.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013825. Topo_IA_cen_sub2.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR013498. Topo_IA_Znf.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR025589. Toprim_C_rpt.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF13368. Toprim_C_rpt. 4 hits.
    PF01396. zf-C4_Topoisom. 1 hit.
    [Graphical view ]
    PRINTSi PR00417. PRTPISMRASEI.
    SMARTi SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56712. SSF56712. 2 hits.
    TIGRFAMsi TIGR01051. topA_bact. 1 hit.
    PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2."
      Chen Y., Crombie A., Rahman M.T., Dedysh S.N., Liesack W., Stott M.B., Alam M., Theisen A.R., Murrell J.C., Dunfield P.F.
      J. Bacteriol. 192:3840-3841(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: BL2 / DSM 15510 / NCIMB 13906Imported.

    Entry informationi

    Entry nameiB8EMQ0_METSB
    AccessioniPrimary (citable) accession number: B8EMQ0
    Entry historyi
    Integrated into UniProtKB/TrEMBL: March 3, 2009
    Last sequence update: March 3, 2009
    Last modified: October 1, 2014
    This is version 47 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