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P68698

- TOP1_VACCW

UniProt

P68698 - TOP1_VACCW

Protein

DNA topoisomerase 1B

Gene

TOP1

Organism
Vaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 69 (01 Oct 2014)
      Sequence version 1 (01 Aug 1988)
      Previous versions | rss
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    Functioni

    Releases the supercoiling and torsional tension of DNA 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 the specific target site 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-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 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.2 Publications

    Catalytic activityi

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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei168 – 1681Involved in religationBy similarity
    Active sitei274 – 2741O-(3'-phospho-DNA)-tyrosine intermediate1 PublicationPROSITE-ProRule annotation

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA topoisomerase type I activity Source: UniProtKB-EC
    3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro

    GO - Biological processi

    1. DNA topological change Source: InterPro

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1B (EC:5.99.1.2)
    Short name:
    TopIB
    Alternative name(s):
    DNA topoisomerase I
    Late protein H6
    Gene namesi
    Name:TOP1
    Ordered Locus Names:VACWR104
    ORF Names:H6R
    OrganismiVaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
    Taxonomic identifieri10254 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePoxviridaeChordopoxvirinaeOrthopoxvirusVaccinia virus
    Virus hostiBos taurus (Bovine) [TaxID: 9913]
    ProteomesiUP000000344: Genome

    Subcellular locationi

    Virion Curated

    GO - Cellular componenti

    1. virion Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Virion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi216 – 2161G → E or K: No change in activity. 1 Publication
    Mutagenesisi217 – 2171I → P: Temperature-sensitive for DNA relaxation in vitro. 1 Publication
    Mutagenesisi220 – 2201K → D: Loss of activity. 1 Publication
    Mutagenesisi220 – 2201K → I or N: Reduced activity. 1 Publication
    Mutagenesisi223 – 2231R → E or G: Loss of activity. 1 Publication
    Mutagenesisi223 – 2231R → K: Reduced activity. 1 Publication
    Mutagenesisi224 – 2241T → G or P: Reduced activity. 1 Publication
    Mutagenesisi225 – 2251Y → H: No change in activity. 1 Publication
    Mutagenesisi225 – 2251Y → R or S: Reduced activity. 1 Publication
    Mutagenesisi274 – 2741Y → F: Complete loss of activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 314314DNA topoisomerase 1BPRO_0000145216Add
    BLAST

    Expressioni

    Inductioni

    Expressed in the late phase of the viral replicative cycle.

    Keywords - Developmental stagei

    Late protein

    Structurei

    Secondary structure

    1
    314
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75
    Beta strandi10 – 145
    Helixi27 – 337
    Beta strandi41 – 466
    Helixi50 – 534
    Beta strandi56 – 627
    Beta strandi68 – 725
    Helixi82 – 10524
    Turni109 – 1113
    Helixi115 – 12511
    Helixi140 – 1467
    Helixi150 – 1523
    Beta strandi153 – 1564
    Beta strandi159 – 1624
    Beta strandi164 – 1663
    Turni167 – 1693
    Beta strandi170 – 1723
    Beta strandi175 – 1773
    Beta strandi180 – 1823
    Helixi183 – 1897
    Beta strandi197 – 2004
    Helixi205 – 21410
    Helixi219 – 24123
    Beta strandi242 – 2443
    Helixi248 – 26316
    Helixi269 – 28214
    Helixi288 – 2925
    Helixi297 – 30913

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A41X-ray2.30A81-314[»]
    1VCCX-ray1.60A1-77[»]
    ProteinModelPortaliP68698.
    SMRiP68698. Positions 1-314.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP68698.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the type IB topoisomerase family.Curated

    Family and domain databases

    Gene3Di1.20.120.380. 1 hit.
    3.30.66.10. 1 hit.
    3.90.15.10. 1 hit.
    InterProiIPR011010. DNA_brk_join_enz.
    IPR001631. TopoI.
    IPR018521. TopoI_AS.
    IPR014711. TopoI_cat_a-hlx-sub_euk.
    IPR027362. TopoI_cat_dom2.
    IPR013500. TopoI_cat_euk.
    IPR015346. TopoI_N_vir.
    [Graphical view]
    PfamiPF01028. Topoisom_I. 1 hit.
    PF09266. VirDNA-topo-I_N. 1 hit.
    [Graphical view]
    PRINTSiPR00416. EUTPISMRASEI.
    SUPFAMiSSF56349. SSF56349. 1 hit.
    PROSITEiPS00176. TOPOISOMERASE_I_EUK. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P68698-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRALFYKDGK LFTDNNFLNP VSDDNPAYEV LQHVKIPTHL TDVVVYEQTW    50
    EEALTRLIFV GSDSKGRRQY FYGKMHVQNR NAKRDRIFVR VYNVMKRINC 100
    FINKNIKKSS TDSNYQLAVF MLMETMFFIR FGKMKYLKEN ETVGLLTLKN 150
    KHIEISPDEI VIKFVGKDKV SHEFVVHKSN RLYKPLLKLT DDSSPEEFLF 200
    NKLSERKVYE CIKQFGIRIK DLRTYGVNYT FLYNFWTNVK SISPLPSPKK 250
    LIALTIKQTA EVVGHTPSIS KRAYMATTIL EMVKDKNFLD VVSKTTFDEF 300
    LSIVVDHVKS STDG 314
    Length:314
    Mass (Da):36,666
    Last modified:August 1, 1988 - v1
    Checksum:iE76FBCFCBF259D27
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M13209 Genomic DNA. Translation: AAB59842.1.
    L13447 Unassigned DNA. Translation: AAA02841.1.
    AY243312 Genomic DNA. Translation: AAO89383.1.
    PIRiG24481. QQVZH7.
    RefSeqiYP_232986.1. NC_006998.1.

    Genome annotation databases

    GeneIDi3707560.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M13209 Genomic DNA. Translation: AAB59842.1 .
    L13447 Unassigned DNA. Translation: AAA02841.1 .
    AY243312 Genomic DNA. Translation: AAO89383.1 .
    PIRi G24481. QQVZH7.
    RefSeqi YP_232986.1. NC_006998.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1A41 X-ray 2.30 A 81-314 [» ]
    1VCC X-ray 1.60 A 1-77 [» ]
    ProteinModelPortali P68698.
    SMRi P68698. Positions 1-314.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 3707560.

    Miscellaneous databases

    EvolutionaryTracei P68698.

    Family and domain databases

    Gene3Di 1.20.120.380. 1 hit.
    3.30.66.10. 1 hit.
    3.90.15.10. 1 hit.
    InterProi IPR011010. DNA_brk_join_enz.
    IPR001631. TopoI.
    IPR018521. TopoI_AS.
    IPR014711. TopoI_cat_a-hlx-sub_euk.
    IPR027362. TopoI_cat_dom2.
    IPR013500. TopoI_cat_euk.
    IPR015346. TopoI_N_vir.
    [Graphical view ]
    Pfami PF01028. Topoisom_I. 1 hit.
    PF09266. VirDNA-topo-I_N. 1 hit.
    [Graphical view ]
    PRINTSi PR00416. EUTPISMRASEI.
    SUPFAMi SSF56349. SSF56349. 1 hit.
    PROSITEi PS00176. TOPOISOMERASE_I_EUK. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Conserved TAAATG sequence at the transcriptional and translational initiation sites of vaccinia virus late genes deduced by structural and functional analysis of the HindIII H genome fragment."
      Rosel J.L., Earl P.L., Weir J.P., Moss B.
      J. Virol. 60:436-449(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Biochemical analysis of mutant alleles of the vaccinia virus topoisomerase I carrying targeted substitutions in a highly conserved domain."
      Klemperer N., Traktman P.
      J. Biol. Chem. 268:15887-15899(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE, MUTAGENESIS.
    3. "Sequencing of the coding region of Vaccinia-WR to an average 9-fold redundancy and an error rate of 0.16/10kb."
      Esposito J.J., Frace A.M., Sammons S.A., Olsen-Rasmussen M., Osborne J., Wohlhueter R.
      Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "Identification of a vaccinia virus gene encoding a type I DNA topoisomerase."
      Shuman S., Moss B.
      Proc. Natl. Acad. Sci. U.S.A. 84:7478-7482(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-22, IDENTIFICATION.
    5. "Analogues of vaccinia virus DNA topoisomerase I modified at the active site tyrosine."
      Gao R., Zhang Y., Choudhury A.K., Dedkova L.M., Hecht S.M.
      J. Am. Chem. Soc. 127:3321-3331(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE, MUTAGENESIS OF TYR-274.
    6. "Major groove interactions of vaccinia Topo I provide specificity by optimally positioning the covalent phosphotyrosine linkage."
      Nagarajan R., Stivers J.T.
      Biochemistry 45:5775-5782(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. "Mechanism and specificity of DNA strand exchange catalyzed by vaccinia DNA topoisomerase type I."
      Stahley M.R., Stivers J.T.
      Biochemistry 49:2786-2795(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6-A resolution."
      Sharma A., Hanai R., Mondragon A.
      Structure 2:767-777(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-77.
    9. "Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases."
      Cheng C., Kussie P., Pavletich N., Shuman S.
      Cell 92:841-850(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 81-314.

    Entry informationi

    Entry nameiTOP1_VACCW
    AccessioniPrimary (citable) accession number: P68698
    Secondary accession number(s): P08585
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: August 1, 1988
    Last modified: October 1, 2014
    This is version 69 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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