DB code: M00158

RLCP classification 3.100.219000.96 : Transfer
CATH domain 3.40.50.140 : Rossmann fold Catalytic domain
1.10.460.10 : Topoisomerase I; domain 2
2.70.20.10 : Topoisomerase I; domain 3
1.10.290.10 : Topoisomerase I; domain 4 Catalytic domain
E.C. 5.99.1.2
CSA 1d6m
M-CSA 1d6m
MACiE M0064

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P14294 DNA topoisomerase 3
EC 5.99.1.2
DNA topoisomerase III
NP_416277.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490024.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01131 (Topoisom_bac)
PF01751 (Toprim)
[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
P14294 TOP3_ECOLI ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00271 C00271
E.C.
Compound Magnesium Single-stranded DNA Single-stranded DNA
Type divalent metal (Ca2+, Mg2+) nucleic acids nucleic acids
ChEBI 18420
PubChem 888
1d6mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1i7dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1d6mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1i7dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1d6mA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1i7dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1d6mA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1i7dA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:C-G-C-A-A-C-T-T(chain B) Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot P06612, literature [5] & [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1d6mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 7;LYS 8
1i7dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 7;LYS 8
1d6mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1i7dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1d6mA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1i7dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1d6mA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 328;ARG 330
1i7dA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ARG 330 mutant Y328F

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.8
[2]
p.1378-1381
[5]
Fig.4, p.1079-1080
[6]
p.200

References
[1]
Resource
Comments
Medline ID
PubMed ID 8621552
Journal J Biol Chem
Year 1996
Volume 271
Pages 9039-45
Authors Zhang HL, Malpure S, Li Z, Hiasa H, DiGate RJ
Title The role of the carboxyl-terminal amino acid residues in Escherichia coli DNA topoisomerase III-mediated catalysis.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10574789
Journal Structure Fold Des
Year 1999
Volume 7
Pages 1373-83
Authors Mondragon A, DiGate R
Title The structure of Escherichia coli DNA topoisomerase III.
Related PDB 1d6m
Related UniProtKB P14294
[3]
Resource
Comments
Medline ID
PubMed ID 10692165
Journal Mol Microbiol
Year 2000
Volume 35
Pages 888-95
Authors Li Z, Mondragon A, Hiasa H, Marians KJ, DiGate RJ
Title Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 11427885
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 583
Authors Feng H
Title Picture story. A DNA acrobat.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 11429611
Journal Nature
Year 2001
Volume 411
Pages 1077-81
Authors Changela A, DiGate RJ, Mondragon A
Title Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule.
Related PDB 1i7d
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 12007989
Journal Trends Pharmacol Sci
Year 2002
Volume 23
Pages 199-201
Authors Champoux JJ
Title A first view of the structure of a type IA topoisomerase with bound DNA.
Related PDB
Related UniProtKB

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:

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