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P46799

- TOP1_THEMA

UniProt

P46799 - TOP1_THEMA

Protein

DNA topoisomerase 1

Gene

topA

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 1 (01 Nov 1995)
      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 bindingi12 – 121Magnesium 1; catalyticUniRule annotation
    Sitei36 – 361Interaction with DNAUniRule annotation
    Metal bindingi84 – 841Magnesium 1; catalyticUniRule annotation
    Metal bindingi84 – 841Magnesium 2UniRule annotation
    Metal bindingi86 – 861Magnesium 2UniRule annotation
    Sitei140 – 1401Interaction with DNAUniRule annotation
    Sitei141 – 1411Interaction with DNAUniRule annotation
    Sitei144 – 1441Interaction with DNAUniRule annotation
    Sitei149 – 1491Interaction with DNAUniRule annotation
    Sitei156 – 1561Interaction with DNAUniRule annotation
    Active sitei288 – 2881O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei290 – 2901Interaction with DNAUniRule annotation
    Sitei475 – 4751Interaction with DNAUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri559 – 58022C4-typeAdd
    BLAST

    GO - Molecular functioni

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

    GO - Biological processi

    1. DNA topological change Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding, Zinc

    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:TM_0258
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 633633DNA topoisomerase 1PRO_0000145169Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi559 ↔ 578
    Disulfide bondi561 ↔ 580

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    STRINGi243274.TM0258.

    Structurei

    Secondary structure

    1
    633
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 125
    Helixi14 – 2411
    Helixi25 – 273
    Beta strandi28 – 325
    Beta strandi37 – 404
    Beta strandi42 – 443
    Beta strandi51 – 555
    Helixi64 – 7613
    Beta strandi79 – 813
    Helixi87 – 9913
    Helixi116 – 1249
    Helixi131 – 15929
    Helixi166 – 18520
    Beta strandi190 – 1989
    Beta strandi201 – 2055
    Helixi215 – 2228
    Beta strandi227 – 23913
    Helixi247 – 25812
    Helixi262 – 27413
    Beta strandi279 – 2835
    Helixi298 – 31114
    Helixi314 – 3163
    Helixi346 – 3494
    Turni350 – 3523
    Helixi355 – 37117
    Beta strandi376 – 38611
    Beta strandi393 – 40311
    Helixi405 – 4084
    Beta strandi431 – 4388
    Helixi447 – 45610
    Turni462 – 4643
    Helixi465 – 47410
    Beta strandi477 – 4815
    Beta strandi484 – 4885
    Helixi489 – 50113
    Turni503 – 5064
    Helixi508 – 52215
    Helixi528 – 54013
    Beta strandi553 – 5586
    Beta strandi560 – 5623
    Beta strandi564 – 5707
    Beta strandi573 – 5775
    Beta strandi579 – 5813
    Beta strandi593 – 5953
    Beta strandi598 – 6003

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GAIX-ray1.70A/B3-633[»]
    2GAJX-ray1.95A/B3-633[»]
    ProteinModelPortaliP46799.
    SMRiP46799. Positions 7-601.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP46799.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini6 – 115110ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni164 – 1696Interaction 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 fingeri559 – 58022C4-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0551.
    KOiK03168.
    OMAiWINKAKK.
    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.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 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]
    ProtoNetiSearch...

    Sequencei

    Sequence statusi: Complete.

    P46799-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKKVKKYIV VESPAKAKTI KSILGNEYEV FASMGHIIDL PKSKFGVDLE    50
    KDFEPEFAVI KGKEKVVEKL KDLAKKGELL IASDMDREGE AIAWHIARVT 100
    NTLGRKNRIV FSEITPRVIR EAVKNPREID MKKVRAQLAR RILDRIVGYS 150
    LSPVLWRNFK SNLSAGRVQS ATLKLVCDRE REILRFVPKK YHRITVNFDG 200
    LTAEIDVKEK KFFDAETLKE IQSIDELVVE EKKVSVKKFA PPEPFKTSTL 250
    QQEAYSKLGF SVSKTMMIAQ QLYEGVETKD GHIAFITYMR TDSTRVSDYA 300
    KEEARNLITE VFGEEYVGSK RERRKSNAKI QDAHEAIRPT NVFMTPEEAG 350
    KYLNSDQKKL YELIWKRFLA SQMKPSQYEE TRFVLRTKDG KYRFKGTVLK 400
    KIFDGYEKVW KTERNTGEFP FEEGESVKPV VVKIEEQETK PKPRYTEGSL 450
    VKEMERLGIG RPSTYASTIK LLLNRGYIKK IRGYLYPTIV GSVVMDYLEK 500
    KYSDVVSVSF TAEMEKDLDE VEQGKKTDKI VLREFYESFS SVFDRNDRIV 550
    VDFPTNQKCS CGKEMRLSFG KYGFYLKCEC GKTRSVKNDE IAVIDDGKIF 600
    LGRKDSESGS PDGRSVEGKG NLSEKRRKGK KGS 633
    Length:633
    Mass (Da):72,695
    Last modified:November 1, 1995 - v1
    Checksum:iF7262A044060CFE9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U27841 Genomic DNA. Translation: AAA68949.1.
    AE000512 Genomic DNA. Translation: AAD35346.1.
    PIRiS62737.
    RefSeqiNP_228071.1. NC_000853.1.
    YP_007976607.1. NC_021214.1.
    YP_008990768.1. NC_023151.1.

    Genome annotation databases

    EnsemblBacteriaiAAD35346; AAD35346; TM_0258.
    GeneIDi897168.
    KEGGitma:TM0258.
    tmi:THEMA_03435.
    tmm:Tmari_0256.
    PATRICi23935393. VBITheMar51294_0262.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U27841 Genomic DNA. Translation: AAA68949.1 .
    AE000512 Genomic DNA. Translation: AAD35346.1 .
    PIRi S62737.
    RefSeqi NP_228071.1. NC_000853.1.
    YP_007976607.1. NC_021214.1.
    YP_008990768.1. NC_023151.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2GAI X-ray 1.70 A/B 3-633 [» ]
    2GAJ X-ray 1.95 A/B 3-633 [» ]
    ProteinModelPortali P46799.
    SMRi P46799. Positions 7-601.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243274.TM0258.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD35346 ; AAD35346 ; TM_0258 .
    GeneIDi 897168.
    KEGGi tma:TM0258.
    tmi:THEMA_03435.
    tmm:Tmari_0256.
    PATRICi 23935393. VBITheMar51294_0262.

    Phylogenomic databases

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

    Miscellaneous databases

    EvolutionaryTracei P46799.

    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.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 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. "Cloning and sequencing of the gene coding for topoisomerase I from the extremely thermophilic eubacterium, Thermotoga maritima."
      Bouthier de la Tour C., Kaltoum H., Portemer C., Confalonieri F., Huber R., Duguet M.
      Biochim. Biophys. Acta 1264:279-283(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    3. "Crystal structure of full length topoisomerase I from Thermotoga maritima."
      Hansen G., Harrenga A., Wieland B., Schomburg D., Reinemer P.
      J. Mol. Biol. 358:1328-1340(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 3-633.

    Entry informationi

    Entry nameiTOP1_THEMA
    AccessioniPrimary (citable) accession number: P46799
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 120 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi