EzCatDB: M00158

DB codeM00158
RLCP classification3.100.219000.96
CATH domainDomain 13.40.50.140Catalytic domain
Domain 21.10.460.10
Domain 32.70.20.10
Domain 41.10.290.10Catalytic domain
E.C.5.99.1.2
CSA1d6m
MACiEM0064

CATH domainRelated DB codes (homologues)
1.10.290.10M00034
1.10.460.10M00034
2.70.20.10M00034
3.40.50.140M00034

Enzyme Name
Swiss-protKEGG

P14294
Protein nameDNA topoisomerase 3DNA 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 III


Swiss-prot:Accession NumberP14294
Entry nameTOP3_ECOLI
ActivityATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subunit
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00271C00271
CompoundMagnesiumSingle-stranded DNASingle-stranded DNA
Typedivalent metal (Ca2+, Mg2+)nucleic acidsnucleic acids
1d6mA01UnboundUnboundUnbound
1i7dA01UnboundUnboundUnbound
1d6mA02UnboundUnboundUnbound
1i7dA02UnboundUnboundUnbound
1d6mA03UnboundUnboundUnbound
1i7dA03UnboundUnboundUnbound
1d6mA04UnboundUnboundUnbound
1i7dA04UnboundBound:C-G-C-A-A-C-T-T(chain B)Unbound

Active-site residues
resource
Swiss-prot P06612, literature [5] & [6]
pdbCatalytic residuescomment
1d6mA01GLU 7;LYS 8

1i7dA01GLU 7;LYS 8

1d6mA02

1i7dA02

1d6mA03

1i7dA03

1d6mA04TYR 328;ARG 330

1i7dA04       ;ARG 330
mutant Y328F

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.8
[2]p.1378-1381
[5]Fig.4, p.1079-1080
[6]p.200

references
[1]
PubMed ID8621552
JournalJ Biol Chem
Year1996
Volume271
Pages9039-45
AuthorsZhang HL, Malpure S, Li Z, Hiasa H, DiGate RJ
TitleThe role of the carboxyl-terminal amino acid residues in Escherichia coli DNA topoisomerase III-mediated catalysis.
[2]
CommentsX-ray crystallography
PubMed ID10574789
JournalStructure Fold Des
Year1999
Volume7
Pages1373-83
AuthorsMondragon A, DiGate R
TitleThe structure of Escherichia coli DNA topoisomerase III.
Related PDB1d6m
Related Swiss-protP14294
[3]
PubMed ID10692165
JournalMol Microbiol
Year2000
Volume35
Pages888-95
AuthorsLi Z, Mondragon A, Hiasa H, Marians KJ, DiGate RJ
TitleIdentification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates.
[4]
PubMed ID11427885
JournalNat Struct Biol
Year2001
Volume8
Pages583
AuthorsFeng H
TitlePicture story. A DNA acrobat.
[5]
PubMed ID11429611
JournalNature
Year2001
Volume411
Pages1077-81
AuthorsChangela A, DiGate RJ, Mondragon A
TitleCrystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule.
Related PDB1i7d
[6]
PubMed ID12007989
JournalTrends Pharmacol Sci
Year2002
Volume23
Pages199-201
AuthorsChampoux JJ
TitleA first view of the structure of a type IA topoisomerase with bound DNA.

comments
This enzyme catalyzes decantenation, which produces two daughter DNA plasmids from replicated plasmids through an intermediate with two linked circular DNA molecules (see [4]).
According to the literature [5] & [6], it catalyzes the following reactions:
(A) Binding of the single-stranded DNA region:
(B) Auto-transfer of DNA segment: 1st step: the cleavage of single-stranded DNA (pre-strand passage):
(B#) Although magnesium ion stimulates the DNA cleavage, it is not required for the reaction.
(B1) Arg330 acts as a modulator, which activates the nucleophile, Tyr328, by lowering its pKa.
(B2) The activated nucleophile, Tyr328, makes a nucleophilic attack on the phosphorus atom of the scissile phosphodiester bond, forming a pentacovalent transition state.
(B3) The negatively charged transition state is stabilized by Lys8 & Arg330.
(B4) Glu7 acts as a general acid to protonate the leaving 3'-hydroxyl group, resulting in the formation of a phosphotyrosine intermediate.
(C) DNA helix passage through the gate, formed by the cleaved DNA:
(B') Auto-transfer of DNA segment: 2nd step: the religation of single-stranded DNA (post-strand passage):
(B1') Glu7 acts as a general base to deprotonate the 3'-hydroxyl group.
(B2') The activated 3'-hydroxyl group makes a nucleophilic attack on the phosphorus atom of the phosphotyrosine intermediate, forming a pentacovalent transition state again.
(B3') The negatively charged transition state is stabilized by Lys8 & Arg330.
(B4') Tyr328 is released.
(D) Relase of the trapped DNA:

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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