DB code: M00034

RLCP classification 3.100.219010.98 : 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
-.-.-.- :
3.30.65.10 : Bacterial Topoisomerase I; domain 1
2.20.25.10 : N-terminal domain of TfIIb
E.C. 5.99.1.2
CSA 1ecl
M-CSA 1ecl
MACiE

CATH domain Related DB codes (homologues)
1.10.290.10 : Topoisomerase I; domain 4 M00158
1.10.460.10 : Topoisomerase I; domain 2 M00158
2.20.25.10 : N-terminal domain of TfIIb M00207
2.70.20.10 : Topoisomerase I; domain 3 M00158
3.40.50.140 : Rossmann fold M00158

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P06612 DNA topoisomerase 1
EC 5.99.1.2
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
NP_415790.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489542.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF08272 (Topo_Zn_Ribbon)
PF01131 (Topoisom_bac)
PF01751 (Toprim)
PF01396 (zf-C4_Topoisom)
[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
P06612 TOP1_ECOLI ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Monomer.

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
 18420
PubChem 888
 888
1cy0A01 Unbound Unbound Unbound
1cy1A01 Unbound Unbound Unbound
1cy2A01 Unbound Unbound Unbound
1cy4A01 Unbound Unbound Unbound
1cy6A01 Unbound Unbound Unbound
1cy7A01 Unbound Unbound Unbound
1cy8A01 Unbound Unbound Unbound
1eclA01 Unbound Unbound Unbound
1mw8X01 Unbound Unbound Unbound
1mw9X01 Unbound Unbound Unbound
1cy0A02 Unbound Unbound Unbound
1cy1A02 Unbound Unbound Unbound
1cy2A02 Unbound Unbound Unbound
1cy4A02 Unbound Unbound Unbound
1cy6A02 Unbound Unbound Unbound
1cy7A02 Unbound Unbound Unbound
1cy8A02 Unbound Unbound Unbound
1eclA02 Unbound Unbound Unbound
1mw8X02 Unbound Unbound Unbound
1mw9X02 Unbound Unbound Unbound
1cy0A03 Unbound Unbound Unbound
1cy1A03 Unbound Unbound Unbound
1cy2A03 Unbound Unbound Unbound
1cy4A03 Unbound Unbound Unbound
1cy6A03 Unbound Unbound Unbound
1cy7A03 Unbound Unbound Unbound
1cy8A03 Unbound Unbound Unbound
1cy9A02 Unbound Unbound Unbound
1cy9B02 Unbound Unbound Unbound
1cyyA02 Unbound Unbound Unbound
1cyyB02 Unbound Unbound Unbound
1eclA03 Unbound Unbound Unbound
1mw8X03 Unbound Unbound Unbound
1mw9X03 Unbound Unbound Unbound
1cy0A04 Unbound Unbound Unbound
1cy1A04 Unbound Unbound Unbound
1cy2A04 Unbound Unbound Unbound
1cy4A04 Unbound Unbound Unbound
1cy6A04 Unbound Unbound Unbound
1cy7A04 Unbound Unbound Unbound
1cy8A04 Unbound Unbound Unbound
1cy9A01 Unbound Unbound Unbound
1cy9B01 Unbound Unbound Unbound
1cyyA01 Unbound Unbound Unbound
1cyyB01 Unbound Unbound Unbound
1eclA04 Unbound Unbound Unbound
1mw8X04 Unbound Bound:C-T-T-C-G-G-G(chain Y) Unbound
1mw9X04 Unbound Unbound Unbound
1yuaA01 Unbound Unbound Unbound
1yuaA02 Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot P06612, literature [8], [11] & [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cy0A01 GLU 9;LYS 13;ASP 111;ARG 136
1cy1A01 GLU 9;LYS 13;ASP 111;ARG 136
1cy2A01 GLU 9;LYS 13;ASP 111;ARG 136
1cy4A01 GLU 9;LYS 13;ASP 111;ARG 136
1cy6A01 GLU 9;LYS 13;ASP 111;ARG 136
1cy7A01 GLU 9;LYS 13;ASP 111;ARG 136
1cy8A01 GLU 9;LYS 13;ASP 111;ARG 136
1eclA01 GLU 9;LYS 13;ASP 111;ARG 136
1mw8X01 GLU 9;LYS 13;ASP 111;ARG 136
1mw9X01 GLU 9;LYS 13;ASP 111;ARG 136
1cy0A02
1cy1A02
1cy2A02
1cy4A02
1cy6A02
1cy7A02
1cy8A02
1eclA02
1mw8X02
1mw9X02
1cy0A03
1cy1A03
1cy2A03
1cy4A03
1cy6A03
1cy7A03
1cy8A03
1cy9A02
1cy9B02
1cyyA02
1cyyB02
1eclA03
1mw8X03
1mw9X03
1cy0A04 TYR 319;ARG 321;HIS 365
1cy1A04 TYR 319;ARG 321;HIS 365
1cy2A04 TYR 319;ARG 321;HIS 365
1cy4A04 TYR 319;ARG 321;HIS 365
1cy6A04 TYR 319;ARG 321;HIS 365
1cy7A04 TYR 319;ARG 321;HIS 365
1cy8A04 TYR 319;ARG 321;HIS 365
1cy9A01 TYR 319;ARG 321;HIS 365
1cy9B01 TYR 319;ARG 321;HIS 365
1cyyA01 TYR 319;ARG 321;HIS 365
1cyyB01 TYR 319;ARG 321;HIS 365
1eclA04 TYR 319;ARG 321;HIS 365
1mw8X04 TYR 319;ARG 321; mutant H365R
1mw9X04 TYR 319;ARG 321; mutant H365R
1yuaA01
1yuaA02

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.5, p.142-145
[8]
[9]
[10]
p.965-967
[11]
p.920-921
[12]
Fig.3
[15]
Fig.2, p.195-198
[17]
Fig.2, p.13243-13245
[18]
Fig.1

References
[1]
Resource
Comments
Medline ID
PubMed ID 2560190
Journal Proteins
Year 1989
Volume 6
Pages 231-9
Authors Lynn RM, Wang JC
Title Peptide sequencing and site-directed mutagenesis identify tyrosine-319 as the active site tyrosine of Escherichia coli DNA topoisomerase I.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1650356
Journal J Biol Chem
Year 1991
Volume 266
Pages 14317-20
Authors Tse-Dinh YC
Title Zinc (II) coordination in Escherichia coli DNA topoisomerase I is required for cleavable complex formation with DNA.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8396651
Journal J Mol Biol
Year 1993
Volume 232
Pages 1213-6
Authors Lima CD, Wang JC, Mondragon A
Title Crystallization of a 67 kDa fragment of Escherichia coli DNA topoisomerase I.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-590.
Medline ID 94159070
PubMed ID 8114910
Journal Nature
Year 1994
Volume 367
Pages 138-46
Authors Lima CD, Wang JC, Mondragon A
Title Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I.
Related PDB 1ecl
Related UniProtKB P06612
[5]
Resource
Comments STRUCTURE BY NMR OF 745-865.
Medline ID 95298771
PubMed ID 7779808
Journal Biochemistry
Year 1995
Volume 34
Pages 7622-8
Authors Yu L, Zhu CX, Tse-Dinh YC, Fesik SW
Title Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I.
Related PDB 1yua
Related UniProtKB P06612
[6]
Resource
Comments
Medline ID
PubMed ID 8703937
Journal Biochemistry
Year 1996
Volume 35
Pages 9661-6
Authors Yu L, Zhu CX, Tse-Dinh YC, Fesik SW
Title Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9792804
Journal Biochem Biophys Res Commun
Year 1998
Volume 251
Pages 509-14
Authors Ahumada A, Tse-Dinh YC
Title The Zn(II) binding motifs of E. coli DNA topoisomerase I is part of a high-affinity DNA binding domain.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9497321
Journal J Biol Chem
Year 1998
Volume 273
Pages 6050-6
Authors Chen SJ, Wang JC
Title Identification of active site residues in Escherichia coli DNA topoisomerase I.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9535856
Journal J Biol Chem
Year 1998
Volume 273
Pages 8783-9
Authors Zhu CX, Roche CJ, Papanicolaou N, DiPietrantonio A, Tse-Dinh YC
Title Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10504732
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 961-8
Authors Feinberg H, Changela A, Mondragon A
Title Protein-nucleotide interactions in E. coli DNA topoisomerase I.
Related PDB 1cy0 1cy1 1cy2 1cy4 1cy6 1cy7 1cy8
Related UniProtKB
[11]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10504724
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 918-22
Authors Feinberg H, Lima CD, Mondragon A
Title Conformational changes in E. coli DNA topoisomerase I.
Related PDB 1cy9 1cyy
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10504717
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 900-2
Authors Keck JL, Berger JM
Title Enzymes that push DNA around.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10873443
Journal J Mol Biol
Year 2000
Volume 299
Pages 1165-77
Authors Grishin NV
Title C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10873470
Journal J Mol Biol
Year 2000
Volume 300
Pages 353-62
Authors Podobnik M, McInerney P, O'Donnell M, Kuriyan J
Title A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11034544
Journal Adv Cancer Res
Year 2001
Volume 80
Pages 189-216
Authors Pourquier P, Pommier Y
Title Topoisomerase I-mediated DNA damage.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11722677
Journal J Clin Pharm Ther
Year 2001
Volume 26
Pages 405-16
Authors Topcu Z
Title DNA topoisomerases as targets for anticancer drugs.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11809772
Journal J Biol Chem
Year 2002
Volume 277
Pages 13237-45
Authors Perry K, Mondragon A
Title Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 14604525
Journal Structure (Camb)
Year 2003
Volume 11
Pages 1349-58
Authors Perry K, Mondragon A
Title Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA.
Related PDB 1mw8 1mw9
Related UniProtKB

Comments
The N-terminal domain structures of this enzyme indicated that it is homologous to DNA topoisomrase III (M00158 in EzCatDB), suggesting that it might have a similar catalytic mechanism to that.
Accoriding to the literature [8], although magnesium ion is required for the activity, it is not required for the DNA cleavage and religation (or Auto-transfer of DNA segment). It might be required for the conformational changes in the enzyme-DNA complexes in the movements of DNA strands (or DNA passage). Arg136 seems to be required for the DNA relaxation activity, despite that it is not involved in the DNA cleavage.
According to the literature [8], [11] & [17], 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#) His365 modulates the pKa of Glu9 through Asp111 (see [17]).
(B1) Arg321 acts as a modulator, which activates the nucleophile, Tyr319, by lowering its pKa.
(B2) The activated nucleophile, Tyr319, 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 Lys13 & Arg321.
(B4) Glu9 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') Glu9 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 Lys13 & Arg321.
(B4') Tyr319 is released.
(D) Relase of the trapped DNA:

Created Updated
2004-04-27 2010-05-14