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P32989

- TOP1_VAR67

UniProt

P32989 - TOP1_VAR67

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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

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
Complete GO annotation...

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

        10         20         30         40         50
MRALFYKDGK LFTDNNFLNP VSDNNPAYEV LQHVKIPTHL TDVVVYGQTW
60 70 80 90 100
EEALTRLIFV GSDSKGRRQY FYGKMHVQNR NAKRDRIFVR VYNVMKRINC
110 120 130 140 150
FINKNIKKSS TDSNYQLAVF MLMETMFFIR FGKMKYLKEN ETVGLLTLKN
160 170 180 190 200
KHIEISPDKI VIKFVGKDKV SHEFVVHKSN RLYKPLLKLT DDSSPEEFLF
210 220 230 240 250
NKLSERKVYE CIKQFGIRIK DLRTYGVNYT FLYNFWTNVK SISPLPSPKK
260 270 280 290 300
LIALTIKQTA EVVGHTPSIS KRAYMATTIL EMVKDKNFLD VVSKTTFDEF
310
LSIVVDHVKS STDG
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

« Hide 'large scale' publications
  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