EzCatDB: M00048
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DB codeM00048
RLCP classification3.100.305000.501 : Transfer
1.15.8230.361 : Hydrolysis
CATH domainDomain 13.30.565.10 : Heat Shock Protein 90Catalytic domain
Domain 23.30.230.10 : Ribosomal Protein S5; domain 2Catalytic domain
Domain 33.30.1490.30 : Dna Ligase; domain 1
Domain 43.40.50.670 : Rossmann foldCatalytic domain
Domain 51.10.268.10 : Topoisomerase; domain 3
Domain 63.30.1360.40 : Gyrase A; domain 2
Domain 73.90.199.10 : Topoisomerase II; domain 5Catalytic domain
E.C.5.99.1.3

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

Enzyme Name
UniProtKBKEGG

P06786
Protein nameDNA topoisomerase 2DNA topoisomerase (ATP-hydrolysing)
type II DNA topoisomerase
DNA-gyrase
deoxyribonucleate topoisomerase
deoxyribonucleic topoisomerase
topoisomerase
DNA topoisomerase II
SynonymsEC 5.99.1.3
DNA topoisomerase II
RefSeqNP_014311.3 (Protein)
NM_001182926.3 (DNA/RNA sequence)
PfamPF00204 (DNA_gyraseB)
PF00521 (DNA_topoisoIV)
PF02518 (HATPase_c)
PF01751 (Toprim)
[Graphical view]


UniProtKB:Accession NumberP06786
Entry nameTOP2_YEAST
ActivityATP-dependent breakage, passage and rejoining of double-stranded DNA.
SubunitHomodimer.
Subcellular locationNucleus.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00434C00002C00001C00434C00008C00009
CompoundMagnesiumDouble-stranded DNAATPH2ODouble-stranded DNAADPOrthophosphate
Typedivalent metal (Ca2+, Mg2+)nucleic acidsamine group,nucleotideH2Onucleic acidsamine group,nucleotidephosphate group/phosphate ion
ChEBI18420

15422
15377

16761
26078
PubChem888

5957
962
22247451

6022
22486802
1004
               
1pvgA01Bound:_MGUnboundAnalogue:ANP UnboundUnboundUnbound
1pvgB01Bound:_MGUnboundAnalogue:ANP UnboundUnboundUnbound
1q1dA01Bound:_MGUnboundAnalogue:ANP UnboundUnboundUnbound
1q1dB01Bound:_MGUnboundAnalogue:ANP UnboundUnboundUnbound
1qzrA01Bound:_MGUnboundAnalogue:ANP UnboundUnboundUnbound
1qzrB01Bound:_MGUnboundAnalogue:ANP UnboundUnboundUnbound
1pvgA02UnboundUnboundUnbound UnboundUnboundUnbound
1pvgB02UnboundUnboundUnbound UnboundUnboundUnbound
1q1dA02UnboundUnboundUnbound UnboundUnboundUnbound
1q1dB02UnboundUnboundUnbound UnboundUnboundUnbound
1qzrA02UnboundUnboundUnbound UnboundUnboundUnbound
1qzrB02UnboundUnboundUnbound UnboundUnboundUnbound
1bgwA01UnboundUnboundUnbound UnboundUnboundUnbound
1bjtA01UnboundUnboundUnbound UnboundUnboundUnbound
1bgwA02UnboundUnboundUnbound UnboundUnboundUnbound
1bjtA02UnboundUnboundUnbound UnboundUnboundUnbound
1bgwA03UnboundUnboundUnbound UnboundUnboundUnbound
1bjtA03UnboundUnboundUnbound UnboundUnboundUnbound
1bgwA04UnboundUnboundUnbound UnboundUnboundUnbound
1bjtA04UnboundUnboundUnbound UnboundUnboundUnbound
1bgwA05UnboundUnboundUnbound UnboundUnboundUnbound
1bjtA05UnboundUnboundUnbound UnboundUnboundUnbound

Active-site residues
resource
Swis-prot;P06786 & literature [15] & [22]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1pvgA01GLU 66
ASN 70(magnesium binding)
ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
 
1pvgB01GLU 66
ASN 70(magnesium binding)
ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
 
1q1dA01GLU 66
ASN 70(magnesium binding)
ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
 
1q1dB01GLU 66
ASN 70(magnesium binding)
ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
 
1qzrA01GLU 66
ASN 70(magnesium binding)
ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
 
1qzrB01GLU 66
ASN 70(magnesium binding)
ARG 141;ASN 142;GLY 143;TYR 144;GLY 145
 
1pvgA02GLN 365;LYS 367
 
 
 
1pvgB02GLN 365;LYS 367
 
 
 
1q1dA02GLN 365;LYS 367
 
 
 
1q1dB02GLN 365;LYS 367
 
 
 
1qzrA02GLN 365;LYS 367
 
 
 
1qzrB02GLN 365;LYS 367
 
 
 
1bgwA01 
 
 
 
1bjtA01 
 
 
 
1bgwA02GLU 450;ASP 531
GLU 450;ASP 527;ASP 529;ASP 531(magnesium ion)
 
invisible 634-682
1bjtA02GLU 449;       
GLU 449;ASP 526;       ;       (magnesium ion)
 
invisible 527-531, 632-652, 660-674
1bgwA03 
 
 
 
1bjtA03 
 
 
 
1bgwA04 
 
 
 
1bjtA04 
 
 
 
1bgwA05ARG 691;ARG 782;TYR 783
 
 
invisible TYR 1085;SER 1086(phospholylation)
1bjtA05ARG 690;ARG 781;TYR 782
 
 
invisible TYR 1086;SER 1087(phospholylation)

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID1654050
JournalBioessays
Year1991
Volume13
Pages269-73
AuthorsOsheroff N, Zechiedrich EL, Gale KC
TitleCatalytic function of DNA topoisomerase II.
[2]
CommentsREVIEW ON PHOSPHORYLATION.
Medline ID93073815
PubMed ID1332607
JournalAntonie Van Leeuwenhoek
Year1992
Volume62
Pages15-24
AuthorsGasser SM, Walter R, Dang Q, Cardenas ME
TitleTopoisomerase II: its functions and phosphorylation.
Related UniProtKBP06786
[3]
PubMed ID7980433
JournalBiochem J
Year1994
Volume303
Pages681-95
AuthorsWatt PM, Hickson ID
TitleStructure and function of type II DNA topoisomerases.
[4]
PubMed ID7893659
JournalBiochemistry
Year1995
Volume34
Pages3632-9
AuthorsLamhasni S, Larsen AK, Barray M, Monnot M, Delain E, Fermandjian S
TitleChanges of self-association, secondary structure, and biological activity properties of topoisomerase II under varying salt conditions.
[5]
PubMed ID8696977
JournalCurr Opin Struct Biol
Year1996
Volume6
Pages84-90
AuthorsBerger JM, Wang JC
TitleRecent developments in DNA topoisomerase II structure and mechanism.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 410-1202.
Medline ID96138378
PubMed ID8538787
JournalNature
Year1996
Volume379
Pages225-32
AuthorsBerger JM, Gamblin SJ, Harrison SC, Wang JC
TitleStructure and mechanism of DNA topoisomerase II.
Related PDB1bgw
Related UniProtKBP06786
[7]
PubMed ID8610153
JournalProc Natl Acad Sci U S A
Year1996
Volume93
Pages2975-80
AuthorsLindsley JE
TitleIntradimerically tethered DNA topoisomerase II is catalytically active in DNA transport.
[8]
PubMed ID8805525
JournalStructure
Year1996
Volume4
Pages117-20
AuthorsWigley DB
TitleA wasp head with a relaxing bite.
[9]
PubMed ID9388273
JournalJ Biol Chem
Year1997
Volume272
Pages31190-5
AuthorsLi W, Wang JC
TitleFootprinting of yeast DNA topoisomerase II lysyl side chains involved in substrate binding and interdomainal interactions.
[10]
PubMed ID9748552
JournalBiochim Biophys Acta
Year1998
Volume1400
Pages155-71
AuthorsAndoh T, Ishida R
TitleCatalytic inhibitors of DNA topoisomerase II.
[11]
PubMed ID9748545
JournalBiochim Biophys Acta
Year1998
Volume1400
Pages139-54
AuthorsBurden DA, Osheroff N
TitleMechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme.
[12]
PubMed ID9710672
JournalClin Infect Dis
Year1998
Volume27 Suppl 1
PagesS54-63
AuthorsHooper DC
TitleBacterial topoisomerases, anti-topoisomerases, and anti-topoisomerase resistance.
[13]
PubMed ID9657678
JournalBiochemistry
Year1998
Volume37
Pages9658-67
AuthorsSmith CV, Maxwell A
TitleIdentification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase.
[14]
PubMed ID10419479
JournalJ Biol Chem
Year1999
Volume274
Pages21688-94
AuthorsOlland S, Wang JC
TitleCatalysis of ATP hydrolysis by two NH(2)-terminal fragments of yeast DNA topoisomerase II.
[15]
CommentsX-ray crystallography
PubMed ID10201398
JournalNat Struct Biol
Year1999
Volume6
Pages322-6
AuthorsFass D, Bogden CE, Berger JM
TitleQuaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands.
Related PDB1bjt
[16]
PubMed ID10380229
JournalPac Symp Biocomput
Year1999
Volume
Pages578-89
AuthorsShaiu WL, Hu T, Hsieh TS
TitleThe hydrophilic, protease-sensitive terminal domains of eucaryotic DNA topoisomerases have essential intracellular functions.
[17]
PubMed ID9927662
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages881-6
AuthorsLiu Q, Wang JC
TitleSimilarity in the catalysis of DNA breakage and rejoining by type IA and IIA DNA topoisomerases.
[18]
PubMed ID10713116
JournalJ Biol Chem
Year2000
Volume275
Pages7980-7
AuthorsDong J, Walker J, Nitiss JL
TitleA mutation in yeast topoisomerase II that confers hypersensitivity to multiple classes of topoisomerase II poisons.
[19]
PubMed ID11090281
JournalJ Mol Biol
Year2000
Volume304
Pages385-95
AuthorsMizushina Y, Sugawara F, Iida A, Sakaguchi K
TitleStructural homology between DNA binding sites of DNA polymerase beta and DNA topoisomerase II.
[20]
PubMed ID10637609
JournalTrends Biochem Sci
Year2000
Volume25
Pages24-8
AuthorsDutta R, Inouye M
TitleGHKL, an emergent ATPase/kinase superfamily.
[21]
PubMed ID12596227
JournalBioessays
Year2003
Volume25
Pages232-42
AuthorsGadelle D, Filee J, Buhler C, Forterre P
TitlePhylogenomics of type II DNA topoisomerases.
[22]
PubMed ID12963818
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages10629-34
AuthorsClassen S, Olland S, Berger JM
TitleStructure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187.
Related PDB1pvg,1q1d,1qzr

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.

createdupdated
2004-04-252010-02-08


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
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