P68698 (TOP1_VACCW) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase 1B
Short name=TopIB
EC=5.99.1.2

Alternative name(s):
DNA topoisomerase I
Late protein H6

Gene names

Name:	TOP1
Ordered Locus Names:	VACWR104
ORF Names:	H6R

Organism

Vaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR)) [Reference proteome]

Taxonomic identifier

10254 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Poxviridae › Chordopoxvirinae › Orthopoxvirus › Vaccinia virus

Virus host

Bos taurus (Bovine) [TaxID: 9913]

Protein attributes

Sequence length	314 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.6 Ref.7
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subcellular location	Virion Potential.
Induction	Expressed in the late phase of the viral replicative cycle.
Sequence similarities	Belongs to the type IB topoisomerase family.

Ontologies

Keywords
Cellular component	Virion
Developmental stage	Late protein
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from electronic annotation. Source: InterPro
Cellular_component	host chromosome Inferred from electronic annotation. Source: InterPro virion Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase type I activity Inferred from electronic annotation. Source: EC DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 314

314

DNA topoisomerase 1B

PRO_0000145216

Sites

Active site

274

1

O-(3'-phospho-DNA)-tyrosine intermediate Ref.5

Site

168

1

Involved in religation By similarity

Experimental info

Mutagenesis

216

1

G → E or K: No change in activity.

Mutagenesis

217

1

I → P: Temperature-sensitive for DNA relaxation in vitro.

Mutagenesis

220

1

K → D: Loss of activity.

Mutagenesis

220

1

K → I or N: Reduced activity.

Mutagenesis

223

1

R → E or G: Loss of activity.

Mutagenesis

223

1

R → K: Reduced activity.

Mutagenesis

224

1

T → G or P: Reduced activity.

Mutagenesis

225

1

Y → H: No change in activity.

Mutagenesis

225

1

Y → R or S: Reduced activity.

Mutagenesis

274

1

Y → F: Complete loss of activity. Ref.5

Secondary structure

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314

Helix Strand Turn

Details...

Beta strand

3 – 7

5

Beta strand

10 – 14

5

Helix

27 – 33

7

Beta strand

41 – 46

6

Helix

50 – 53

4

Beta strand

56 – 62

7

Beta strand

68 – 72

5

Helix

82 – 105

24

Turn

109 – 111

3

Helix

115 – 125

11

Helix

140 – 146

7

Helix

150 – 152

3

Beta strand

153 – 156

4

Beta strand

159 – 162

4

Beta strand

164 – 166

3

Turn

167 – 169

3

Beta strand

170 – 172

3

Beta strand

175 – 177

3

Beta strand

180 – 182

3

Helix

183 – 189

7

Beta strand

197 – 200

4

Helix

205 – 214

10

Helix

219 – 241

23

Beta strand

242 – 244

3

Helix

248 – 263

16

Helix

269 – 282

14

Helix

288 – 292

5

Helix

297 – 309

13

Sequences

	Sequence		Length	Mass (Da)
	P68698 [UniParc]. Last modified August 1, 1988. Version 1. Checksum: E76FBCFCBF259D27	FASTA	314	36,666
	10 20 30 40 50 60 MRALFYKDGK LFTDNNFLNP VSDDNPAYEV LQHVKIPTHL TDVVVYEQTW EEALTRLIFV 70 80 90 100 110 120 GSDSKGRRQY FYGKMHVQNR NAKRDRIFVR VYNVMKRINC FINKNIKKSS TDSNYQLAVF 130 140 150 160 170 180 MLMETMFFIR FGKMKYLKEN ETVGLLTLKN KHIEISPDEI VIKFVGKDKV SHEFVVHKSN 190 200 210 220 230 240 RLYKPLLKLT DDSSPEEFLF NKLSERKVYE CIKQFGIRIK DLRTYGVNYT FLYNFWTNVK 250 260 270 280 290 300 SISPLPSPKK LIALTIKQTA EVVGHTPSIS KRAYMATTIL EMVKDKNFLD VVSKTTFDEF 310 LSIVVDHVKS STDG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M13209 Genomic DNA. Translation: AAB59842.1.
L13447 Unassigned DNA. Translation: AAA02841.1.
AY243312 Genomic DNA. Translation: AAO89383.1.

PIR

QQVZH7. G24481.

RefSeq

YP_232986.1. NC_006998.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A41	X-ray	2.30	A	81-314	[»]
1VCC	X-ray	1.60	A	1-77	[»]

ProteinModelPortal

P68698.

SMR

P68698. Positions 1-314.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

3707560.

Phylogenomic databases

ProtClustDB

PHA3101.

Family and domain databases

Gene3D

3.30.66.10. 1 hit.
3.90.15.10. 1 hit.

InterPro

IPR011010. DNA_brk_join_enz.
IPR001631. TopoI.
IPR018521. TopoI_AS.
IPR014711. TopoI_cat_a-hlx-sub_euk.
IPR013500. TopoI_cat_euk.
IPR015346. TopoI_N_vir.
[Graphical view]

Pfam

PF01028. Topoisom_I. 1 hit.
PF09266. VirDNA-topo-I_N. 1 hit.
[Graphical view]

PRINTS

PR00416. EUTPISMRASEI.

SUPFAM

SSF56349. DNA_brk_join_enz. 1 hit.

PROSITE

PS00176. TOPOISOMERASE_I_EUK. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P68698.

Entry information

Entry name

TOP1_VACCW

Accession

Primary (citable) accession number: P68698
Secondary accession number(s): P08585

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1988
Last modified:	April 3, 2013
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program