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O73954

- TOP1_PYRFU

UniProt

O73954 - TOP1_PYRFU

Protein

DNA topoisomerase 1

Gene

topA

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 118 (01 Oct 2014)
      Sequence version 2 (26 Sep 2001)
      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 By similarity.By similarity

    Catalytic activityi

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

    Cofactori

    Magnesium. Binds two Mg2+ per subunit By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi7 – 71Magnesium 1; catalyticBy similarity
    Sitei52 – 521Interaction with DNABy similarity
    Metal bindingi107 – 1071Magnesium 1; catalyticBy similarity
    Metal bindingi107 – 1071Magnesium 2By similarity
    Metal bindingi109 – 1091Magnesium 2By similarity
    Sitei166 – 1661Interaction with DNABy similarity
    Sitei170 – 1701Interaction with DNABy similarity
    Active sitei690 – 6901O-(5'-phospho-DNA)-tyrosine intermediateBy similarity
    Sitei692 – 6921Interaction with DNABy similarity
    Sitei880 – 8801Interaction with DNABy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri978 – 100629C4-type 1Add
    BLAST
    Zinc fingeri1025 – 105026C4-type 2; atypicalAdd
    BLAST

    GO - Molecular functioni

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

    GO - Biological processi

    1. DNA topological change Source: UniProtKB-HAMAP
    2. intein-mediated protein splicing Source: InterPro
    3. intron homing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Isomerase, Nuclease, Topoisomerase

    Keywords - Biological processi

    Intron homing

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1 (EC:5.99.1.2)
    Alternative name(s):
    DNA topoisomerase I
    Omega-protein
    Relaxing enzyme
    Swivelase
    Untwisting enzyme
    Cleaved into the following chain:
    Alternative name(s):
    Pfu topA intein
    Gene namesi
    Name:topA
    Ordered Locus Names:PF0494
    OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
    Taxonomic identifieri186497 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000001013: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 314314DNA topoisomerase 1, 1st partPRO_0000034794Add
    BLAST
    Chaini315 – 687373Endonuclease PI-PfuISequence AnalysisPRO_0000034795Add
    BLAST
    Chaini688 – 1060373DNA topoisomerase 1, 2nd partPRO_0000034796Add
    BLAST

    Post-translational modificationi

    This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

    Keywords - PTMi

    Autocatalytic cleavage, Protein splicing

    Proteomic databases

    PRIDEiO73954.

    Interactioni

    Subunit structurei

    Monomer.By similarity

    Protein-protein interaction databases

    STRINGi186497.PF0494.

    Structurei

    3D structure databases

    ProteinModelPortaliO73954.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 141141ToprimAdd
    BLAST
    Domaini482 – 591110DOD-type homing endonucleaseAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni196 – 2016Interaction with DNABy similarity

    Sequence similaritiesi

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

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri978 – 100629C4-type 1Add
    BLAST
    Zinc fingeri1025 – 105026C4-type 2; atypicalAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0551.
    HOGENOMiHOG000004019.
    KOiK03168.
    OMAiDYHNFIA.

    Family and domain databases

    Gene3Di1.10.290.10. 1 hit.
    1.10.460.10. 2 hits.
    2.170.16.10. 2 hits.
    2.70.20.10. 2 hits.
    3.40.50.140. 1 hit.
    HAMAPiMF_00952. Topoisom_1_prok.
    InterProiIPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR006142. INTEIN.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_splice_site.
    IPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013825. Topo_IA_cen_sub2.
    IPR013826. Topo_IA_cen_sub3.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR013498. Topo_IA_Znf.
    IPR005739. TopoI_arch.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF01131. Topoisom_bac. 2 hits.
    PF01751. Toprim. 1 hit.
    PF01396. zf-C4_Topoisom. 1 hit.
    [Graphical view]
    PRINTSiPR00379. INTEIN.
    PR00417. PRTPISMRASEI.
    SMARTiSM00305. HintC. 1 hit.
    SM00306. HintN. 1 hit.
    SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view]
    SUPFAMiSSF51294. SSF51294. 3 hits.
    SSF56712. SSF56712. 2 hits.
    TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
    TIGR01445. intein_Nterm. 1 hit.
    TIGR01057. topA_arch. 2 hits.
    PROSITEiPS50818. INTEIN_C_TER. 1 hit.
    PS50819. INTEIN_ENDONUCLEASE. 1 hit.
    PS50817. INTEIN_N_TER. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    O73954-1 [UniParc]FASTAAdd to Basket

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    MILVIAEKPN VARKIAMALA EVKPIKKTLF GVPYYELIRD GKRLIVASAV     50
    GHLYGLAPKN DFFGYPIFDV EWVPVYIAEK GKEYAKDYIK LLSVLSKRVR 100
    EFIVACDYDT EGEVIGYTAL KYACGVDPGV AKRMKFSALT KRDLIKAWYN 150
    LEPTINFGMA NAGIARHILD WYWGVNLSRA LTHAIKRASG KWVVLSTGRV 200
    QGPTLKFLVD REREIQSFVP QPYWVIKLIF EKNGKKYTAN YEKDKIWDEN 250
    EAKRIVLEVK KAPARVTNIE VKQQNRNPPV PFDLGTLQRE AYSAFGFSPK 300
    KTLDIAQSLY EKGFCLHPDT LILTSQGVRK IKELSREGEV FALDFNLKLS 350
    KAKYRLLERD ADEQMYKVTL LDGTELYLTA DHPVLVYREG NLAFVPADKL 400
    RETDHVVLVL NKSARDNYGF LDLLLEITDS QEDYAILENG ETLSLHSLKM 450
    LVERGEIKDI AVVGFSHNNF GKVMLRDELW YLIGYLAGKG GEIKGNGVVI 500
    SSRTKEIVGL TKSLNIDLIE TEEGIVLSNK SFVRLLHLIH YTPRVPEVYG 550
    IINNTEWLKA FLAGYYDATL LEGLTLEALY KIKVYLQLLG IRAKIEDNKL 600
    KVHLEDLQRF RELLGKFSRR KLYVETSQVP VFTDFDERSY DFPRILGGDI 650
    YIIGIKSIEK FHYKGKVYDL VVENYHNFIA NGIAVHNCSY PRTESQKLPK 700
    NLNYKFIIQN LARIPEYRPY AHLLLGMPEL KPVEGKKEDP AHPAIYPTGE 750
    IPRPGDLTKD EALLYDMIVR RFLAVFMEPA VRETVKVTIS AGKHKFFISG 800
    GRTVKEGWLR VYGKYVKFDE VTLPTFFIGE RIKVLQVKRE KKKTKPPARY 850
    SPAAVIKKME DLGLGTKATR AQILETLYQR GYIEGKKSIK VTPLGMKVIE 900
    TLEKYVPEII SVELTREFEK KMELIMEGKL TKEEVIEEAK IRLTKILEEF 950
    KKKELEIGLE LAKIVVGEEK PPLIVGKCPK CGGDLIVKYN EKTGKRFVGC 1000
    SNWPKCNVTY PILQRGEIIP TNKTCCNGAP VVIIREKDGR EWEICLDMNC 1050
    KEYNTIKKKR 1060
    Length:1,060
    Mass (Da):121,182
    Last modified:September 26, 2001 - v2
    Checksum:i81D815333D51C0BC
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti218 – 2181F → L in AAC26106. (PubMed:9524230)Curated
    Sequence conflicti235 – 2351K → E in AAC26106. (PubMed:9524230)Curated
    Sequence conflicti293 – 2931S → P in AAC26106. (PubMed:9524230)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009950 Genomic DNA. Translation: AAL80618.1.
    AF042825 Genomic DNA. Translation: AAC26106.1.
    RefSeqiNP_578223.1. NC_003413.1.

    Genome annotation databases

    EnsemblBacteriaiAAL80618; AAL80618; PF0494.
    GeneIDi1468335.
    KEGGipfu:PF0494.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009950 Genomic DNA. Translation: AAL80618.1 .
    AF042825 Genomic DNA. Translation: AAC26106.1 .
    RefSeqi NP_578223.1. NC_003413.1.

    3D structure databases

    ProteinModelPortali O73954.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 186497.PF0494.

    Proteomic databases

    PRIDEi O73954.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL80618 ; AAL80618 ; PF0494 .
    GeneIDi 1468335.
    KEGGi pfu:PF0494.

    Phylogenomic databases

    eggNOGi COG0551.
    HOGENOMi HOG000004019.
    KOi K03168.
    OMAi DYHNFIA.

    Family and domain databases

    Gene3Di 1.10.290.10. 1 hit.
    1.10.460.10. 2 hits.
    2.170.16.10. 2 hits.
    2.70.20.10. 2 hits.
    3.40.50.140. 1 hit.
    HAMAPi MF_00952. Topoisom_1_prok.
    InterProi IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR006142. INTEIN.
    IPR004042. Intein_endonuc.
    IPR006141. Intein_splice_site.
    IPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013825. Topo_IA_cen_sub2.
    IPR013826. Topo_IA_cen_sub3.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR013498. Topo_IA_Znf.
    IPR005739. TopoI_arch.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF01131. Topoisom_bac. 2 hits.
    PF01751. Toprim. 1 hit.
    PF01396. zf-C4_Topoisom. 1 hit.
    [Graphical view ]
    PRINTSi PR00379. INTEIN.
    PR00417. PRTPISMRASEI.
    SMARTi SM00305. HintC. 1 hit.
    SM00306. HintN. 1 hit.
    SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51294. SSF51294. 3 hits.
    SSF56712. SSF56712. 2 hits.
    TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
    TIGR01445. intein_Nterm. 1 hit.
    TIGR01057. topA_arch. 2 hits.
    PROSITEi PS50818. INTEIN_C_TER. 1 hit.
    PS50819. INTEIN_ENDONUCLEASE. 1 hit.
    PS50817. INTEIN_N_TER. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
      Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
      Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    2. "A topA intein in Pyrococcus furiosus and its relatedness to the r-gyr intein of Methanococcus jannaschii."
      Chute I.C., Hu Z., Liu X.-Q.
      Gene 210:85-92(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 127-1060.

    Entry informationi

    Entry nameiTOP1_PYRFU
    AccessioniPrimary (citable) accession number: O73954
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2001
    Last sequence update: September 26, 2001
    Last modified: October 1, 2014
    This is version 118 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    When a topoisomerase transiently breaks a DNA backbone bond, it simultaneously forms a protein-DNA link, in which a tyrosyl oxygen in the enzyme is joined to a DNA phosphorus at one end of the enzyme-severed DNA strand.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Intein-containing proteins
      List of intein-containing protein entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3