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
(B1') Glu7 acts as a general base to deprotonate the 3'-hydroxyl group.
(B') Auto-transfer of DNA segment: 2nd step: the religation of single-stranded DNA (post-strand passage):
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:
(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