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P32989

- TOP1_VAR67

UniProt

P32989 - TOP1_VAR67

Protein

DNA topoisomerase 1

Gene

TOP1

Organism
Variola virus (isolate Human/India/Ind3/1967) (VARV) (Smallpox virus)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 86 (01 Oct 2014)
      Sequence version 1 (01 Oct 1993)
      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 By similarity.By similarity

    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 religationCurated
    Active sitei274 – 2741O-(3'-phospho-DNA)-tyrosine intermediate

    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 1 (EC:5.99.1.2)
    Alternative name(s):
    DNA topoisomerase I
    Gene namesi
    Name:TOP1
    ORF Names:H6R, I6R
    OrganismiVariola virus (isolate Human/India/Ind3/1967) (VARV) (Smallpox virus)
    Taxonomic identifieri587200 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePoxviridaeChordopoxvirinaeOrthopoxvirus
    Virus hostiHomo sapiens (Human) [TaxID: 9606]
    ProteomesiUP000002060: Genome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi168 – 1681D → A: Increased DNA-binding affinity, inhibition of product release, defective in relaxation of supercoiled plasmid substrates. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 314314DNA topoisomerase 1PRO_0000145217Add
    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 – 488
    Helixi50 – 534
    Beta strandi56 – 627
    Beta strandi68 – 725
    Helixi74 – 10532
    Helixi113 – 12715
    Helixi134 – 1407
    Helixi150 – 1523
    Beta strandi153 – 1564
    Beta strandi159 – 1657
    Helixi167 – 1693
    Beta strandi171 – 1777
    Helixi183 – 1897
    Beta strandi197 – 2004
    Helixi205 – 2128
    Helixi213 – 2153
    Helixi219 – 24123
    Beta strandi242 – 2443
    Helixi248 – 26316
    Turni267 – 2693
    Helixi270 – 2734
    Helixi276 – 2827
    Helixi288 – 2936
    Helixi297 – 31115

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2H7FX-ray2.70X1-314[»]
    2H7GX-ray1.90X1-314[»]
    3IGCX-ray2.10A1-314[»]
    ProteinModelPortaliP32989.
    SMRiP32989. Positions 1-314.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP32989.

    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.

    P32989-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRALFYKDGK LFTDNNFLNP VSDNNPAYEV LQHVKIPTHL TDVVVYGQTW    50
    EEALTRLIFV GSDSKGRRQY FYGKMHVQNR NAKRDRIFVR VYNVMKRINC 100
    FINKNIKKSS TDSNYQLAVF MLMETMFFIR FGKMKYLKEN ETVGLLTLKN 150
    KHIEISPDKI VIKFVGKDKV SHEFVVHKSN RLYKPLLKLT DDSSPEEFLF 200
    NKLSERKVYE CIKQFGIRIK DLRTYGVNYT FLYNFWTNVK SISPLPSPKK 250
    LIALTIKQTA EVVGHTPSIS KRAYMATTIL EMVKDKNFLD VVSKTTFDEF 300
    LSIVVDHVKS STDG 314
    Length:314
    Mass (Da):36,592
    Last modified:October 1, 1993 - v1
    Checksum:iAE9C7DC5FA363BEE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X67119 Genomic DNA. Translation: CAA47588.1.
    S55844 Genomic DNA. Translation: AAB24685.1.
    X69198 Genomic DNA. Translation: CAA49030.1.
    PIRiE36846.
    RefSeqiNP_042133.1. NC_001611.1.

    Genome annotation databases

    GeneIDi1486444.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X67119 Genomic DNA. Translation: CAA47588.1 .
    S55844 Genomic DNA. Translation: AAB24685.1 .
    X69198 Genomic DNA. Translation: CAA49030.1 .
    PIRi E36846.
    RefSeqi NP_042133.1. NC_001611.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2H7F X-ray 2.70 X 1-314 [» ]
    2H7G X-ray 1.90 X 1-314 [» ]
    3IGC X-ray 2.10 A 1-314 [» ]
    ProteinModelPortali P32989.
    SMRi P32989. Positions 1-314.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1486444.

    Miscellaneous databases

    EvolutionaryTracei P32989.

    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. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Genes of variola and vaccinia viruses necessary to overcome the host protective mechanisms."
      Shchelkunov S.N., Blinov V.M., Sandakhchiev L.S.
      FEBS Lett. 319:80-83(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes."
      Minkah N., Hwang Y., Perry K., Van Duyne G.D., Hendrickson R., Lefkowitz E.J., Hannenhalli S., Bushman F.D.
      Virology 365:60-69(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    4. "Structural basis for specificity in the poxvirus topoisomerase."
      Perry K., Hwang Y., Bushman F.D., Van Duyne G.D.
      Mol. Cell 23:343-354(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), MUTAGENESIS OF ASP-168.
    5. "Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic."
      Perry K., Hwang Y., Bushman F.D., Van Duyne G.D.
      Structure 18:127-137(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

    Entry informationi

    Entry nameiTOP1_VAR67
    AccessioniPrimary (citable) accession number: P32989
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: October 1, 1993
    Last modified: October 1, 2014
    This is version 86 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, 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