EzCatDB: M00034

DB codeM00034
RLCP classification3.100.219010.98
CATH domainDomain 13.40.50.140Catalytic domain
Domain 21.10.460.10
Domain 32.70.20.10
Domain 41.10.290.10Catalytic domain
Domain 5-.-.-.-
Domain 63.30.65.10
Domain 72.20.25.10
E.C.5.99.1.2
CSA1ecl

CATH domainRelated DB codes (homologues)
1.10.290.10M00158
1.10.460.10M00158
2.20.25.10M00207
2.70.20.10M00158
3.40.50.140M00158

Enzyme Name
Swiss-protKEGG

P06612
Protein nameDNA topoisomerase 1DNA 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 I
Omega-protein
Relaxing enzyme
Untwisting enzyme
Swivelase


Swiss-prot:Accession NumberP06612
Entry nameTOP1_ECOLI
ActivityATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
SubunitMonomer.
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00271C00271
CompoundMagnesiumSingle-stranded DNASingle-stranded DNA
Typedivalent metal (Ca2+, Mg2+)nucleic acidsnucleic acids
1cy0A01UnboundUnboundUnbound
1cy1A01UnboundUnboundUnbound
1cy2A01UnboundUnboundUnbound
1cy4A01UnboundUnboundUnbound
1cy6A01UnboundUnboundUnbound
1cy7A01UnboundUnboundUnbound
1cy8A01UnboundUnboundUnbound
1eclA01UnboundUnboundUnbound
1mw8X01UnboundUnboundUnbound
1mw9X01UnboundUnboundUnbound
1cy0A02UnboundUnboundUnbound
1cy1A02UnboundUnboundUnbound
1cy2A02UnboundUnboundUnbound
1cy4A02UnboundUnboundUnbound
1cy6A02UnboundUnboundUnbound
1cy7A02UnboundUnboundUnbound
1cy8A02UnboundUnboundUnbound
1eclA02UnboundUnboundUnbound
1mw8X02UnboundUnboundUnbound
1mw9X02UnboundUnboundUnbound
1cy0A03UnboundUnboundUnbound
1cy1A03UnboundUnboundUnbound
1cy2A03UnboundUnboundUnbound
1cy4A03UnboundUnboundUnbound
1cy6A03UnboundUnboundUnbound
1cy7A03UnboundUnboundUnbound
1cy8A03UnboundUnboundUnbound
1cy9A02UnboundUnboundUnbound
1cy9B02UnboundUnboundUnbound
1cyyA02UnboundUnboundUnbound
1cyyB02UnboundUnboundUnbound
1eclA03UnboundUnboundUnbound
1mw8X03UnboundUnboundUnbound
1mw9X03UnboundUnboundUnbound
1cy0A04UnboundUnboundUnbound
1cy1A04UnboundUnboundUnbound
1cy2A04UnboundUnboundUnbound
1cy4A04UnboundUnboundUnbound
1cy6A04UnboundUnboundUnbound
1cy7A04UnboundUnboundUnbound
1cy8A04UnboundUnboundUnbound
1cy9A01UnboundUnboundUnbound
1cy9B01UnboundUnboundUnbound
1cyyA01UnboundUnboundUnbound
1cyyB01UnboundUnboundUnbound
1eclA04UnboundUnboundUnbound
1mw8X04UnboundBound:C-T-T-C-G-G-G(chain Y)Unbound
1mw9X04UnboundUnboundUnbound
1yuaA01UnboundUnboundUnbound
1yuaA02UnboundUnboundUnbound

Active-site residues
resource
Swiss-prot P06612, literature [8], [11] & [17]
pdbCatalytic residuescomment
1cy0A01GLU 9;LYS 13;ASP 111;ARG 136

1cy1A01GLU 9;LYS 13;ASP 111;ARG 136

1cy2A01GLU 9;LYS 13;ASP 111;ARG 136

1cy4A01GLU 9;LYS 13;ASP 111;ARG 136

1cy6A01GLU 9;LYS 13;ASP 111;ARG 136

1cy7A01GLU 9;LYS 13;ASP 111;ARG 136

1cy8A01GLU 9;LYS 13;ASP 111;ARG 136

1eclA01GLU 9;LYS 13;ASP 111;ARG 136

1mw8X01GLU 9;LYS 13;ASP 111;ARG 136

1mw9X01GLU 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

1cy0A04TYR 319;ARG 321;HIS 365

1cy1A04TYR 319;ARG 321;HIS 365

1cy2A04TYR 319;ARG 321;HIS 365

1cy4A04TYR 319;ARG 321;HIS 365

1cy6A04TYR 319;ARG 321;HIS 365

1cy7A04TYR 319;ARG 321;HIS 365

1cy8A04TYR 319;ARG 321;HIS 365

1cy9A01TYR 319;ARG 321;HIS 365

1cy9B01TYR 319;ARG 321;HIS 365

1cyyA01TYR 319;ARG 321;HIS 365

1cyyB01TYR 319;ARG 321;HIS 365

1eclA04TYR 319;ARG 321;HIS 365

1mw8X04TYR 319;ARG 321;       
mutant H365R
1mw9X04TYR 319;ARG 321;       
mutant H365R
1yuaA01

1yuaA02


References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID2560190
JournalProteins
Year1989
Volume6
Pages231-9
AuthorsLynn RM, Wang JC
TitlePeptide sequencing and site-directed mutagenesis identify tyrosine-319 as the active site tyrosine of Escherichia coli DNA topoisomerase I.
[2]
PubMed ID1650356
JournalJ Biol Chem
Year1991
Volume266
Pages14317-20
AuthorsTse-Dinh YC
TitleZinc (II) coordination in Escherichia coli DNA topoisomerase I is required for cleavable complex formation with DNA.
[3]
PubMed ID8396651
JournalJ Mol Biol
Year1993
Volume232
Pages1213-6
AuthorsLima CD, Wang JC, Mondragon A
TitleCrystallization of a 67 kDa fragment of Escherichia coli DNA topoisomerase I.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-590.
Medline ID94159070
PubMed ID8114910
JournalNature
Year1994
Volume367
Pages138-46
AuthorsLima CD, Wang JC, Mondragon A
TitleThree-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I.
Related PDB1ecl
Related Swiss-protP06612
[5]
CommentsSTRUCTURE BY NMR OF 745-865.
Medline ID95298771
PubMed ID7779808
JournalBiochemistry
Year1995
Volume34
Pages7622-8
AuthorsYu L, Zhu CX, Tse-Dinh YC, Fesik SW
TitleSolution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I.
Related PDB1yua
Related Swiss-protP06612
[6]
PubMed ID8703937
JournalBiochemistry
Year1996
Volume35
Pages9661-6
AuthorsYu L, Zhu CX, Tse-Dinh YC, Fesik SW
TitleBackbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA.
[7]
PubMed ID9792804
JournalBiochem Biophys Res Commun
Year1998
Volume251
Pages509-14
AuthorsAhumada A, Tse-Dinh YC
TitleThe Zn(II) binding motifs of E. coli DNA topoisomerase I is part of a high-affinity DNA binding domain.
[8]
PubMed ID9497321
JournalJ Biol Chem
Year1998
Volume273
Pages6050-6
AuthorsChen SJ, Wang JC
TitleIdentification of active site residues in Escherichia coli DNA topoisomerase I.
[9]
PubMed ID9535856
JournalJ Biol Chem
Year1998
Volume273
Pages8783-9
AuthorsZhu CX, Roche CJ, Papanicolaou N, DiPietrantonio A, Tse-Dinh YC
TitleSite-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I.
[10]
CommentsX-ray crystallography
PubMed ID10504732
JournalNat Struct Biol
Year1999
Volume6
Pages961-8
AuthorsFeinberg H, Changela A, Mondragon A
TitleProtein-nucleotide interactions in E. coli DNA topoisomerase I.
Related PDB1cy0,1cy1,1cy2,1cy4,1cy6,1cy7,1cy8
[11]
CommentsX-ray crystallography
PubMed ID10504724
JournalNat Struct Biol
Year1999
Volume6
Pages918-22
AuthorsFeinberg H, Lima CD, Mondragon A
TitleConformational changes in E. coli DNA topoisomerase I.
Related PDB1cy9,1cyy
[12]
PubMed ID10504717
JournalNat Struct Biol
Year1999
Volume6
Pages900-2
AuthorsKeck JL, Berger JM
TitleEnzymes that push DNA around.
[13]
PubMed ID10873443
JournalJ Mol Biol
Year2000
Volume299
Pages1165-77
AuthorsGrishin NV
TitleC-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily.
[14]
PubMed ID10873470
JournalJ Mol Biol
Year2000
Volume300
Pages353-62
AuthorsPodobnik M, McInerney P, O'Donnell M, Kuriyan J
TitleA TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases.
[15]
PubMed ID11034544
JournalAdv Cancer Res
Year2001
Volume80
Pages189-216
AuthorsPourquier P, Pommier Y
TitleTopoisomerase I-mediated DNA damage.
[16]
PubMed ID11722677
JournalJ Clin Pharm Ther
Year2001
Volume26
Pages405-16
AuthorsTopcu Z
TitleDNA topoisomerases as targets for anticancer drugs.
[17]
PubMed ID11809772
JournalJ Biol Chem
Year2002
Volume277
Pages13237-45
AuthorsPerry K, Mondragon A
TitleBiochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis.
[18]
PubMed ID14604525
JournalStructure (Camb)
Year2003
Volume11
Pages1349-58
AuthorsPerry K, Mondragon A
TitleStructure of a complex between E. coli DNA topoisomerase I and single-stranded DNA.
Related PDB1mw8,1mw9

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:

createdupdated
2004-04-272010-05-14


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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