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Q9KRB2

- TOP1_VIBCH

UniProt

Q9KRB2 - TOP1_VIBCH

Protein

DNA topoisomerase 1

Gene

topA

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 105 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      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 annotation

    Catalytic activityi

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

    Cofactori

    Magnesium. Binds two Mg2+ per subunit.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi9 – 91Magnesium 1; catalyticUniRule annotation
    Sitei33 – 331Interaction with DNAUniRule annotation
    Metal bindingi119 – 1191Magnesium 1; catalyticUniRule annotation
    Metal bindingi119 – 1191Magnesium 2UniRule annotation
    Metal bindingi121 – 1211Magnesium 2UniRule annotation
    Sitei176 – 1761Interaction with DNAUniRule annotation
    Sitei177 – 1771Interaction with DNAUniRule annotation
    Sitei180 – 1801Interaction with DNAUniRule annotation
    Sitei192 – 1921Interaction with DNAUniRule annotation
    Active sitei327 – 3271O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei329 – 3291Interaction with DNAUniRule annotation
    Sitei514 – 5141Interaction with DNAUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri668 – 69528C4-type 1Add
    BLAST
    Zinc fingeri717 – 74226C4-type 2Add
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA topoisomerase type I activity Source: TIGR
    3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro
    4. magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. DNA topological change Source: TIGR

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciVCHO:VC1730-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
    Alternative name(s):
    DNA topoisomerase IUniRule annotation
    Omega-protein
    Relaxing enzyme
    Swivelase
    Untwisting enzyme
    Gene namesi
    Name:topAUniRule annotation
    Ordered Locus Names:VC_1730
    OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
    Taxonomic identifieri243277 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
    ProteomesiUP000000584: Chromosome 1

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 876876DNA topoisomerase 1PRO_0000145171Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    STRINGi243277.VC1730.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9KRB2.
    SMRiQ9KRB2. Positions 2-579, 751-867.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini3 – 150148ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni200 – 2056Interaction with DNAUniRule annotation

    Sequence similaritiesi

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

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri668 – 69528C4-type 1Add
    BLAST
    Zinc fingeri717 – 74226C4-type 2Add
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0551.
    KOiK03168.
    OMAiVVECDKC.
    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.
    IPR013263. TopoI_Znr_bac.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
    PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    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. 1 hit.
    TIGRFAMsiTIGR01051. topA_bact. 1 hit.
    PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9KRB2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGKSLVIVES PAKAKTINKY LGKDFIVKSS VGHVRDLPTA GQTATPTGKA    50
    AAASTKKAST TDKEQQKREK ERAALIKKMG VDPYHGWQAN YQILPGKEKV 100
    VAELQKLAKD ADSVYLATDL DREGEAIAWH LREIIGGDEK RYKRVVFNEI 150
    TKNAIQQAFK QPGELNMDGV NAQQARRFMD RVVGFMVSPL LWKKVARGLS 200
    AGRVQSVAVK LLVEREREIK AFVPEEFWDI NADTLTADKQ DFRLLVAQKD 250
    GLAFKPVNET EALAAVAALN KAQYEVCKRE DKPTTSKPSA PFITSTLQQA 300
    ASTRLGYGVK KTMMLAQRLY EAGYITYMRT DSTNLSAEAV ENLRGYITKH 350
    YGEAYLPSQP NVYGSKQNAQ EAHEAIRPSD VTVTADDLEG MEADAHKLYA 400
    LIWNQFVACQ MTPAQYDSTT VSVKAAEYTL KAKGRILKFD GWTRVQRPLG 450
    KNEDQILPPV KVGDSLKLVS LDPKQHFTKP PARYTEAALV KELEKRGIGR 500
    PSTYASIIST IQDRGYVKVD QRRFFAEKMG EIVTDRLDEN FDDLMNYDFT 550
    ARMEEKLDQI AEGEVNWTAV LDEFFADFSR DLETAEQDES LGGMKPNHIV 600
    MTNILCPTCS RPMGIRTAST GVFLGCSGYG LPPKERCKTT INLGDEEGVI 650
    NVLEEDVETA ALRAKKRCPI CETAMDAYLI DDKRKLHVCG NNPNCEGFIV 700
    EEGEFKVKGY EGPTVECDKC GSDMVLKNGR FGKYMGCTND ACKNTRKILK 750
    NGEVAPPKEE PVHFPELPCE NSDAYFVLRD GASGLFFAAS NFPKSRETRA 800
    PLVEELKRFA ERLPEKYQYL TSAPAHDPDG LPAVVRFSRK EKEHYVRTET 850
    EGKPSGWMAV YQEGKWLVTD KRKNAK 876
    Length:876
    Mass (Da):97,910
    Last modified:October 1, 2000 - v1
    Checksum:i8A5BC9148CA1B753
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003852 Genomic DNA. Translation: AAF94880.1.
    PIRiB82163.
    RefSeqiNP_231366.1. NC_002505.1.

    Genome annotation databases

    EnsemblBacteriaiAAF94880; AAF94880; VC_1730.
    GeneIDi2613735.
    KEGGivch:VC1730.
    PATRICi20082518. VBIVibCho83274_1655.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003852 Genomic DNA. Translation: AAF94880.1 .
    PIRi B82163.
    RefSeqi NP_231366.1. NC_002505.1.

    3D structure databases

    ProteinModelPortali Q9KRB2.
    SMRi Q9KRB2. Positions 2-579, 751-867.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243277.VC1730.

    Protocols and materials databases

    DNASUi 2613735.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAF94880 ; AAF94880 ; VC_1730 .
    GeneIDi 2613735.
    KEGGi vch:VC1730.
    PATRICi 20082518. VBIVibCho83274_1655.

    Phylogenomic databases

    eggNOGi COG0551.
    KOi K03168.
    OMAi VVECDKC.
    OrthoDBi EOG6S7XQ9.

    Enzyme and pathway databases

    BioCyci VCHO:VC1730-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.
    IPR013263. TopoI_Znr_bac.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF08272. Topo_Zn_Ribbon. 2 hits.
    PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    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. 1 hit.
    TIGRFAMsi TIGR01051. topA_bact. 1 hit.
    PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 39315 / El Tor Inaba N16961.

    Entry informationi

    Entry nameiTOP1_VIBCH
    AccessioniPrimary (citable) accession number: Q9KRB2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 105 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3