EzCatDB: M00158
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DB codeM00158
RLCP classification3.100.219000.96 : Transfer
CATH domainDomain 13.40.50.140 : Rossmann foldCatalytic domain
Domain 21.10.460.10 : Topoisomerase I; domain 2
Domain 32.70.20.10 : Topoisomerase I; domain 3
Domain 41.10.290.10 : Topoisomerase I; domain 4Catalytic domain
E.C.5.99.1.2
CSA1d6m
MACiEM0064

CATH domainRelated DB codes (homologues)
1.10.290.10 : Topoisomerase I; domain 4M00034
1.10.460.10 : Topoisomerase I; domain 2M00034
2.70.20.10 : Topoisomerase I; domain 3M00034
3.40.50.140 : Rossmann foldM00034

Enzyme Name
UniProtKBKEGG

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
RefSeqNP_416277.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490024.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01131 (Topoisom_bac)
PF01751 (Toprim)
[Graphical view]


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

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00271C00271
CompoundMagnesiumSingle-stranded DNASingle-stranded DNA
Typedivalent metal (Ca2+, Mg2+)nucleic acidsnucleic acids
ChEBI18420


PubChem888


           
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 UniProtKBP14294
[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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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