EzCatDB: T00228

DB codeT00228
CATH domainDomain 13.30.66.10
Domain 23.90.15.10
Domain 31.20.120.380Catalytic domain
E.C.5.99.1.2
MACiEM0232

CATH domainRelated DB codes (homologues)
3.90.15.10M00047,M00182

Enzyme Name
Swiss-protKEGG

P68698
Protein nameDNA topoisomerase 1DNA topoisomerase
type I DNA topoisomerase
untwisting enzyme
relaxing enzyme
nicking-closing enzyme
swivelase
omega-protein
deoxyribonucleate topoisomerase
topoisomerase
type I DNA topoisomerase
SynonymsEC 5.99.1.2
DNA topoisomerase I
Late protein H7


Swiss-prot:Accession NumberP68698
Entry nameTOP1_VACCV
ActivityATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00271C00271
CompoundSingle-stranded DNASingle-stranded DNA
Typenucleic acidsnucleic acids
1vccAUnboundUnbound
1a41A01UnboundUnbound
1a41A02UnboundUnbound

Active-site residues
resource
Swiss-prot;P08585
pdbCatalytic residues
1vccA
1a41A01
1a41A02TYR 274

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID2852543
JournalCell Biol Int Rep
Year1988
Volume12
Pages927-30
AuthorsHolmstrom M
TitleHomology at a possible catalytic site in DNA topoisomerase I.
[2]
PubMed ID1846364
JournalJ Biol Chem
Year1991
Volume266
Pages1796-803
AuthorsShuman S
TitleSite-specific DNA cleavage by vaccinia virus DNA topoisomerase I. Role of nucleotide sequence and DNA secondary structure.
[3]
PubMed ID1314832
JournalJ Biol Chem
Year1992
Volume267
Pages8620-7
AuthorsShuman S
TitleDNA strand transfer reactions catalyzed by vaccinia topoisomerase I.
[4]
PubMed ID7803409
JournalBiochemistry
Year1994
Volume33
Pages15449-58
AuthorsStivers JT, Shuman S, Mildvan AS
TitleVaccinia DNA topoisomerase I: kinetic evidence for general acid-base catalysis and a conformational step.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-77
Medline ID95086864
PubMed ID7994576
JournalStructure
Year1994
Volume2
Pages767-77
AuthorsSharma A, Hanai R, Mondragon A
TitleCrystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution.
Related PDB1vcc
Related Swiss-protP08585
[6]
PubMed ID7744804
JournalJ Biol Chem
Year1995
Volume270
Pages11636-45
AuthorsSekiguchi J, Shuman S
TitleProteolytic footprinting of vaccinia topoisomerase bound to DNA.
[7]
PubMed ID8670847
JournalEMBO J
Year1996
Volume15
Pages3448-57
AuthorsSekiguchi J, Shuman S
TitleIdentification of contacts between topoisomerase I and its target DNA by site-specific photocrosslinking.
[8]
PubMed ID9020090
JournalJ Biol Chem
Year1997
Volume272
Pages3891-6
AuthorsPetersen BO, Shuman S
TitleHistidine 265 is important for covalent catalysis by vaccinia topoisomerase and is conserved in all eukaryotic type I enzymes.
[9]
PubMed ID9188465
JournalJ Biol Chem
Year1997
Volume272
Pages15721-8
AuthorsSekiguchi J, Cheng C, Shuman S
TitleKinetic analysis of DNA and RNA strand transfer reactions catalyzed by vaccinia topoisomerase.
[10]
PubMed ID9224599
JournalNucleic Acids Res
Year1997
Volume25
Pages3001-8
AuthorsWittschieben J, Shuman S
TitleMechanism of DNA transesterification by vaccinia topoisomerase: catalytic contributions of essential residues Arg-130, Gly-132, Tyr-136 and Lys-167.
[11]
PubMed ID9748643
JournalBiochim Biophys Acta
Year1998
Volume1400
Pages321-37
AuthorsShuman S
TitleVaccinia virus DNA topoisomerase: a model eukaryotic type IB enzyme.
[12]
PubMed ID9529259
JournalCell
Year1998
Volume92
Pages841-50
AuthorsCheng C, Kussie P, Pavletich N, Shuman S
TitleConservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases.
Related PDB1a41
[13]
PubMed ID9565576
JournalJ Biol Chem
Year1998
Volume273
Pages11589-95
AuthorsCheng C, Shuman S
TitleA catalytic domain of eukaryotic DNA topoisomerase I.
[14]
PubMed ID9421505
JournalNucleic Acids Res
Year1998
Volume26
Pages490-6
AuthorsWittschieben J, Petersen BO, Shuman S
TitleReplacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease.
[15]
PubMed ID10047584
JournalCurr Opin Struct Biol
Year1999
Volume9
Pages29-36
AuthorsRedinbo MR, Champoux JJ, Hol WG
TitleStructural insights into the function of type IB topoisomerases.
[16]
PubMed ID10911997
JournalMol Cell
Year2000
Volume5
Pages1035-41
AuthorsKrogh BO, Shuman S
TitleCatalytic mechanism of DNA topoisomerase IB.
[17]
PubMed ID10954601
JournalNucleic Acids Res
Year2000
Volume28
Pages3323-31
AuthorsWoodfield G, Cheng C, Shuman S, Burgin AB
TitleVaccinia topoisomerase and Cre recombinase catalyze direct ligation of activated DNA substrates containing a 3'-para-nitrophenyl phosphate ester.
[18]
PubMed ID11441004
JournalJ Biol Chem
Year2001
Volume276
Pages36091-9
AuthorsKrogh BO, Shuman S
TitleVaccinia topoisomerase mutants illuminate conformational changes during closure of the protein clamp and assembly of a functional active site.
[19]
PubMed ID11756402
JournalJ Biol Chem
Year2002
Volume277
Pages5711-4
AuthorsKrogh BO, Shuman S
TitleProton relay mechanism of general acid catalysis by DNA topoisomerase IB.
[20]
PubMed ID11830640
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages1853-8
AuthorsKrogh BO, Shuman S
TitleA poxvirus-like type IB topoisomerase family in bacteria.

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

createdupdated
2004-04-272009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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