DB code: T00228

CATH domain 3.30.66.10 : Viral Topoisomerase I
3.90.15.10 : Topoisomerase I; Chain A, domain 3
1.20.120.380 : Four Helix Bundle (Hemerythrin (Met), subunit A) Catalytic domain
E.C. 5.99.1.2
CSA
M-CSA
MACiE M0232

CATH domain Related DB codes (homologues)
3.90.15.10 : Topoisomerase I; Chain A, domain 3 M00047 M00182

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P68698 DNA topoisomerase 1
EC 5.99.1.2
DNA topoisomerase I
Late protein H7
YP_232986.1 (Protein)
NC_006998.1 (DNA/RNA sequence)
PF01028 (Topoisom_I)
PF09266 (VirDNA-topo-I_N)
[Graphical View]

KEGG enzyme name
DNA topoisomerase
type I DNA topoisomerase
untwisting enzyme
relaxing enzyme
nicking-closing enzyme
swivelase
omega-protein
deoxyribonucleate topoisomerase
topoisomerase
type I DNA topoisomerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P68698 TOP1_VACCV ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00271 C00271
E.C.
Compound Single-stranded DNA Single-stranded DNA
Type nucleic acids nucleic acids
ChEBI
PubChem
1vccA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1a41A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1a41A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P08585

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1vccA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1a41A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1a41A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 274

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.8626-8627
[4]
Fig.6A, p.15456-15457
[8]
[10]
p.3007-3008
[11]
Fig.2, p.322-335
[12]
p.845-846
[14]
Fig.10
[15]
p.33
[16]
Fig.1
[17]
p.3327
[19]

References
[1]
Resource
Comments
Medline ID
PubMed ID 2852543
Journal Cell Biol Int Rep
Year 1988
Volume 12
Pages 927-30
Authors Holmstrom M
Title Homology at a possible catalytic site in DNA topoisomerase I.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1846364
Journal J Biol Chem
Year 1991
Volume 266
Pages 1796-803
Authors Shuman S
Title Site-specific DNA cleavage by vaccinia virus DNA topoisomerase I. Role of nucleotide sequence and DNA secondary structure.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1314832
Journal J Biol Chem
Year 1992
Volume 267
Pages 8620-7
Authors Shuman S
Title DNA strand transfer reactions catalyzed by vaccinia topoisomerase I.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7803409
Journal Biochemistry
Year 1994
Volume 33
Pages 15449-58
Authors Stivers JT, Shuman S, Mildvan AS
Title Vaccinia DNA topoisomerase I: kinetic evidence for general acid-base catalysis and a conformational step.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-77
Medline ID 95086864
PubMed ID 7994576
Journal Structure
Year 1994
Volume 2
Pages 767-77
Authors Sharma A, Hanai R, Mondragon A
Title Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution.
Related PDB 1vcc
Related UniProtKB P08585
[6]
Resource
Comments
Medline ID
PubMed ID 7744804
Journal J Biol Chem
Year 1995
Volume 270
Pages 11636-45
Authors Sekiguchi J, Shuman S
Title Proteolytic footprinting of vaccinia topoisomerase bound to DNA.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8670847
Journal EMBO J
Year 1996
Volume 15
Pages 3448-57
Authors Sekiguchi J, Shuman S
Title Identification of contacts between topoisomerase I and its target DNA by site-specific photocrosslinking.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9020090
Journal J Biol Chem
Year 1997
Volume 272
Pages 3891-6
Authors Petersen BO, Shuman S
Title Histidine 265 is important for covalent catalysis by vaccinia topoisomerase and is conserved in all eukaryotic type I enzymes.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9188465
Journal J Biol Chem
Year 1997
Volume 272
Pages 15721-8
Authors Sekiguchi J, Cheng C, Shuman S
Title Kinetic analysis of DNA and RNA strand transfer reactions catalyzed by vaccinia topoisomerase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9224599
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 3001-8
Authors Wittschieben J, Shuman S
Title Mechanism of DNA transesterification by vaccinia topoisomerase: catalytic contributions of essential residues Arg-130, Gly-132, Tyr-136 and Lys-167.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9748643
Journal Biochim Biophys Acta
Year 1998
Volume 1400
Pages 321-37
Authors Shuman S
Title Vaccinia virus DNA topoisomerase: a model eukaryotic type IB enzyme.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 9529259
Journal Cell
Year 1998
Volume 92
Pages 841-50
Authors Cheng C, Kussie P, Pavletich N, Shuman S
Title Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases.
Related PDB 1a41
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9565576
Journal J Biol Chem
Year 1998
Volume 273
Pages 11589-95
Authors Cheng C, Shuman S
Title A catalytic domain of eukaryotic DNA topoisomerase I.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9421505
Journal Nucleic Acids Res
Year 1998
Volume 26
Pages 490-6
Authors Wittschieben J, Petersen BO, Shuman S
Title Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10047584
Journal Curr Opin Struct Biol
Year 1999
Volume 9
Pages 29-36
Authors Redinbo MR, Champoux JJ, Hol WG
Title Structural insights into the function of type IB topoisomerases.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10911997
Journal Mol Cell
Year 2000
Volume 5
Pages 1035-41
Authors Krogh BO, Shuman S
Title Catalytic mechanism of DNA topoisomerase IB.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10954601
Journal Nucleic Acids Res
Year 2000
Volume 28
Pages 3323-31
Authors Woodfield G, Cheng C, Shuman S, Burgin AB
Title Vaccinia topoisomerase and Cre recombinase catalyze direct ligation of activated DNA substrates containing a 3'-para-nitrophenyl phosphate ester.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11441004
Journal J Biol Chem
Year 2001
Volume 276
Pages 36091-9
Authors Krogh BO, Shuman S
Title Vaccinia topoisomerase mutants illuminate conformational changes during closure of the protein clamp and assembly of a functional active site.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11756402
Journal J Biol Chem
Year 2002
Volume 277
Pages 5711-4
Authors Krogh BO, Shuman S
Title Proton relay mechanism of general acid catalysis by DNA topoisomerase IB.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11830640
Journal Proc Natl Acad Sci U S A
Year 2002
Volume 99
Pages 1853-8
Authors Krogh BO, Shuman S
Title A poxvirus-like type IB topoisomerase family in bacteria.
Related PDB
Related UniProtKB

Comments
This enzyme is composed of N-terminal region (PDB;1vcc) and C-terminal catalytic region (PDB;1a41), which seems to have two domains.

Created Updated
2004-04-27 2009-02-26