DB code: M00048

RLCP classification 3.100.305000.501 : Transfer
1.15.8230.361 : Hydrolysis
CATH domain 3.30.565.10 : Heat Shock Protein 90 Catalytic domain
3.30.230.10 : Ribosomal Protein S5; domain 2 Catalytic domain
3.30.1490.30 : Dna Ligase; domain 1
3.40.50.670 : Rossmann fold Catalytic domain
1.10.268.10 : Topoisomerase; domain 3
3.30.1360.40 : Gyrase A; domain 2
3.90.199.10 : Topoisomerase II; domain 5 Catalytic domain
E.C. 5.99.1.3
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.268.10 : Topoisomerase; domain 3 M00137
3.30.1360.40 : Gyrase A; domain 2 M00137
3.30.230.10 : Ribosomal Protein S5; domain 2 T00244 M00213
3.30.565.10 : Heat Shock Protein 90 M00213
3.90.199.10 : Topoisomerase II; domain 5 M00137

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P06786 DNA topoisomerase 2
EC 5.99.1.3
DNA topoisomerase II
NP_014311.3 (Protein)
NM_001182926.3 (DNA/RNA sequence)
PF00204 (DNA_gyraseB)
PF00521 (DNA_topoisoIV)
PF02518 (HATPase_c)
PF01751 (Toprim)
[Graphical View]

KEGG enzyme name
DNA topoisomerase (ATP-hydrolysing)
type II DNA topoisomerase
DNA-gyrase
deoxyribonucleate topoisomerase
deoxyribonucleic topoisomerase
topoisomerase
DNA topoisomerase II

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P06786 TOP2_YEAST ATP-dependent breakage, passage and rejoining of double-stranded DNA. Homodimer. Nucleus.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00434 C00002 C00001 C00434 C00008 C00009
E.C.
Compound Magnesium Double-stranded DNA ATP H2O Double-stranded DNA ADP Orthophosphate
Type divalent metal (Ca2+, Mg2+) nucleic acids amine group,nucleotide H2O nucleic acids amine group,nucleotide phosphate group/phosphate ion
ChEBI 18420
15422
15377
16761
26078
PubChem 888
5957
22247451
962
6022
1004
22486802
1pvgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:ANP Unbound Unbound Unbound
1pvgB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:ANP Unbound Unbound Unbound
1q1dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:ANP Unbound Unbound Unbound
1q1dB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:ANP Unbound Unbound Unbound
1qzrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:ANP Unbound Unbound Unbound
1qzrB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:ANP Unbound Unbound Unbound
1pvgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1pvgB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1q1dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1q1dB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qzrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qzrB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bgwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bjtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bgwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bjtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bgwA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bjtA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bgwA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bjtA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bgwA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bjtA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swis-prot;P06786 & literature [15] & [22]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1pvgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 66 ASN 70(magnesium binding) ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
1pvgB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 66 ASN 70(magnesium binding) ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
1q1dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 66 ASN 70(magnesium binding) ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
1q1dB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 66 ASN 70(magnesium binding) ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
1qzrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 66 ASN 70(magnesium binding) ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
1qzrB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 66 ASN 70(magnesium binding) ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
1pvgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 365;LYS 367
1pvgB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 365;LYS 367
1q1dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 365;LYS 367
1q1dB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 365;LYS 367
1qzrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 365;LYS 367
1qzrB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 365;LYS 367
1bgwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bjtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bgwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 450;ASP 531 GLU 450;ASP 527;ASP 529;ASP 531(magnesium ion) invisible 634-682
1bjtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 449; GLU 449;ASP 526; ; (magnesium ion) invisible 527-531, 632-652, 660-674
1bgwA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bjtA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bgwA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bjtA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bgwA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 691;ARG 782;TYR 783 invisible TYR 1085;SER 1086(phospholylation)
1bjtA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 690;ARG 781;TYR 782 invisible TYR 1086;SER 1087(phospholylation)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.1, p.271-272
[3]
Fig.3
[5]
Fig.4, p.85-87
[6]
Fig.5
[10]
Fig.3, p.157-158
[11]
Fig.2, p.142-144
[15]
p.323-325
[17]
p.886
[20]
p.271-272
[22]
p.10631

References
[1]
Resource
Comments
Medline ID
PubMed ID 1654050
Journal Bioessays
Year 1991
Volume 13
Pages 269-73
Authors Osheroff N, Zechiedrich EL, Gale KC
Title Catalytic function of DNA topoisomerase II.
Related PDB
Related UniProtKB
[2]
Resource
Comments REVIEW ON PHOSPHORYLATION.
Medline ID 93073815
PubMed ID 1332607
Journal Antonie Van Leeuwenhoek
Year 1992
Volume 62
Pages 15-24
Authors Gasser SM, Walter R, Dang Q, Cardenas ME
Title Topoisomerase II: its functions and phosphorylation.
Related PDB
Related UniProtKB P06786
[3]
Resource
Comments
Medline ID
PubMed ID 7980433
Journal Biochem J
Year 1994
Volume 303
Pages 681-95
Authors Watt PM, Hickson ID
Title Structure and function of type II DNA topoisomerases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7893659
Journal Biochemistry
Year 1995
Volume 34
Pages 3632-9
Authors Lamhasni S, Larsen AK, Barray M, Monnot M, Delain E, Fermandjian S
Title Changes of self-association, secondary structure, and biological activity properties of topoisomerase II under varying salt conditions.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8696977
Journal Curr Opin Struct Biol
Year 1996
Volume 6
Pages 84-90
Authors Berger JM, Wang JC
Title Recent developments in DNA topoisomerase II structure and mechanism.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 410-1202.
Medline ID 96138378
PubMed ID 8538787
Journal Nature
Year 1996
Volume 379
Pages 225-32
Authors Berger JM, Gamblin SJ, Harrison SC, Wang JC
Title Structure and mechanism of DNA topoisomerase II.
Related PDB 1bgw
Related UniProtKB P06786
[7]
Resource
Comments
Medline ID
PubMed ID 8610153
Journal Proc Natl Acad Sci U S A
Year 1996
Volume 93
Pages 2975-80
Authors Lindsley JE
Title Intradimerically tethered DNA topoisomerase II is catalytically active in DNA transport.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8805525
Journal Structure
Year 1996
Volume 4
Pages 117-20
Authors Wigley DB
Title A wasp head with a relaxing bite.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9388273
Journal J Biol Chem
Year 1997
Volume 272
Pages 31190-5
Authors Li W, Wang JC
Title Footprinting of yeast DNA topoisomerase II lysyl side chains involved in substrate binding and interdomainal interactions.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9748552
Journal Biochim Biophys Acta
Year 1998
Volume 1400
Pages 155-71
Authors Andoh T, Ishida R
Title Catalytic inhibitors of DNA topoisomerase II.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9748545
Journal Biochim Biophys Acta
Year 1998
Volume 1400
Pages 139-54
Authors Burden DA, Osheroff N
Title Mechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 9710672
Journal Clin Infect Dis
Year 1998
Volume 27 Suppl 1
Pages S54-63
Authors Hooper DC
Title Bacterial topoisomerases, anti-topoisomerases, and anti-topoisomerase resistance.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9657678
Journal Biochemistry
Year 1998
Volume 37
Pages 9658-67
Authors Smith CV, Maxwell A
Title Identification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10419479
Journal J Biol Chem
Year 1999
Volume 274
Pages 21688-94
Authors Olland S, Wang JC
Title Catalysis of ATP hydrolysis by two NH(2)-terminal fragments of yeast DNA topoisomerase II.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10201398
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 322-6
Authors Fass D, Bogden CE, Berger JM
Title Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands.
Related PDB 1bjt
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10380229
Journal Pac Symp Biocomput
Year 1999
Volume
Pages 578-89
Authors Shaiu WL, Hu T, Hsieh TS
Title The hydrophilic, protease-sensitive terminal domains of eucaryotic DNA topoisomerases have essential intracellular functions.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 9927662
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 881-6
Authors Liu Q, Wang JC
Title Similarity in the catalysis of DNA breakage and rejoining by type IA and IIA DNA topoisomerases.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 10713116
Journal J Biol Chem
Year 2000
Volume 275
Pages 7980-7
Authors Dong J, Walker J, Nitiss JL
Title A mutation in yeast topoisomerase II that confers hypersensitivity to multiple classes of topoisomerase II poisons.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11090281
Journal J Mol Biol
Year 2000
Volume 304
Pages 385-95
Authors Mizushina Y, Sugawara F, Iida A, Sakaguchi K
Title Structural homology between DNA binding sites of DNA polymerase beta and DNA topoisomerase II.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 10637609
Journal Trends Biochem Sci
Year 2000
Volume 25
Pages 24-8
Authors Dutta R, Inouye M
Title GHKL, an emergent ATPase/kinase superfamily.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12596227
Journal Bioessays
Year 2003
Volume 25
Pages 232-42
Authors Gadelle D, Filee J, Buhler C, Forterre P
Title Phylogenomics of type II DNA topoisomerases.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12963818
Journal Proc Natl Acad Sci U S A
Year 2003
Volume 100
Pages 10629-34
Authors Classen S, Olland S, Berger JM
Title Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187.
Related PDB 1pvg 1q1d 1qzr
Related UniProtKB

Comments
This enzyme is composed of ATPase region, which is responsible for hydrolysis of ATP, and topoisomerase region, which is responsible for intramolecular transfer reaction of DNA molecule (DNA binding and clevage). The PDB structures, 1pvg, 1q1d, & 1qzr, correspond to the ATPase region, whilst the rest of PDB structures, 1bgw & 1bjt, correspond to the topoisomeraes region. The topoisomerase region can be divided into the N-terminal B' fragment (residues 410-679) and C-terminal A' fragment (residues 680-1202). The structure of the C-terminal domain with phosphorylation sites has not been determined yet.
The literature [22] describes the roles and the relationships between the two functional regions, ATPase and topisomerase regions.
According to the literature [10] & [11], the catalytic cycle of this enzyme proceeds as follows:
(A) DNA binding: A pair of DNA duplexes bind to the enzyme. Here, the DNA duplex that will be cleaved is called G-segment of DNA, whilst the other DNA duplex that will be transported is called T-segment.
(B) The cleavage of G-segment (pre-strand passage): At this step, active-site tyrosine (Tyr783 of 1bgw) residues at the dimer of A' fragment make nucleophilic attacks on the 5'-terminal phosphate groups of the DNA broken sites, to form covalent bonds with the G-segment, by leaving 4-base stagger. This reaction requires magnesium ion, which must be bound to cluster of acidic residues (Glu450, Asp527, Asp529 & Asp531 of 1bgw) (see [15]).
According to the literature [17], this trans-esterfication proceeds as follows:
(B1) Either Glu450 or Asp531 (of 1bgw) from other protomer (of the dimer) assists the active-site tyrosine, Tyr783, probably by abstracting a proton from the phenol group.
(B2) The activated Tyr783 makes a nucleophilic attack on the phosphate of G-segment, to form a covalent bond. At this step, Arg690 and Arg650 (from the other chain) probably stabilize the transtion-state together with magnesium ion bound to the acidic residues
(However, the tertiary structure of the dimer complex is not available, and it is difficult to confirm that these residues are close enough.)
(C) DNA strand passage: ATP binding to the N-terminal ATPase domain converts the enzyme to a closed protein clamp, by inducing the dimerization of the N-terminal domain (see [5]). During the dimerization, the enzyme domains capture the second DNA duplex (T-segment), and push it into the interior of the enzyme and through the DNA gate, made by the cleavage of the first DNA duplex (G-segment) (see [6]).
(B') The religation of G-segment (post-strand passage): The reverse reaction of the cleavage. (Possibly, the hydroxyl group of 3'-end of DNA makes a nucleophilic attack on the phosphate group linked to the active-site tyrosine residues.)
(D) ATP hydrolysis: ATP hydrolysis triggers the opening of the protein clamp, releasing the DNA product (T-segment). According to the literature [13] & [20], the ATP hydrolysis (at ATPase) proceeds as follows;
(D1) Glu66 (of 1pvg) acts as a general base, to activate a water molecule, which must be in-line for a nucleophilic attack on the gamma-phosphate of ATP. Lys367 may stabilize the activated water during this reaction.
(D2) Lys367 stabilizes the transition-state, along with mainchain amide of resdiues 141-145. Magnesium ion, bound to Asn70, stabilizes the transition-state.

Created Updated
2004-04-25 2010-02-08