EzCatDB: D00077

DB codeD00077
RLCP classification3.770.220000.47
CATH domainDomain 12.30.37.60
Domain 21.10.10.10Catalytic domain
E.C.2.1.1.63
CSA1eh6
MACiEM0251

CATH domainRelated DB codes (homologues)
1.10.10.10D00510,D00452,D00517,T00055,T00113

Enzyme Name
Swiss-protKEGG

P16455
Protein nameMethylated-DNA--protein-cysteine methyltransferasemethylated-DNA---[protein]-cysteine S-methyltransferase
SynonymsEC 2.1.1.63
6-O-methylguanine-DNA methyltransferase
MGMT
O-6-methylguanine-DNA-alkyltransferase


Swiss-prot:Accession NumberP16455
Entry nameMGMT_HUMAN
ActivityDNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L- cysteine.
Subunit
Subcellular locationNucleus.
CofactorBinds 1 zinc ion.


SubstratesProducts
KEGG-idC04250C02743C00039C03800
CompoundDNA containing 6-O-methylguanineProtein cysteineDNAProtein S-methyl-L-cysteine
Typeamine group,carbohydrate,nucleic acidspeptide/protein,sulfhydryl groupnucleic acidspeptide/protein,sulfide group
1eh6A01UnboundUnboundUnboundUnbound
1eh7A01UnboundUnboundUnboundUnbound
1eh8A01UnboundUnboundUnboundUnbound
1qntA01UnboundUnboundUnboundUnbound
1eh6A02UnboundUnboundUnboundUnbound
1eh7A02UnboundUnboundUnboundBound:SMC
1eh8A02UnboundUnboundUnboundAnalogue:BCS
1qntA02UnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P16455 & literature
pdbCatalytic residuesModified residues
1eh6A01

1eh7A01

1eh8A01

1qntA01

1eh6A02TYR 114;ASN 137;CYS 145;HIS 146;GLU 172
                   
1eh7A02TYR 114;ASN 137;       ;HIS 146;GLU 172
SMC 145(methylated)
1eh8A02TYR 114;ASN 137;       ;HIS 146;GLU 172
BCS 145(alkylated) 
1qntA02TYR 114;ASN 137;CYS 145;HIS 146;GLU 172
                   

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Figure 5, p.93191
[3]Fig.3, p.1498, p.1499
[11]Scheme 2, p.6805-6806
[13]Fig.5, p.17271

references
[1]
PubMed ID3174452
JournalNucleic Acids Res
Year1988
Volume16
Pages9307-21
AuthorsYamagata Y, Kohda K, Tomita K
TitleStructural studies of O6-methyldeoxyguanosine and related compounds: a promutagenic DNA lesion by methylating carcinogens.
[2]
PubMed ID2164681
JournalProc Natl Acad Sci U S A
Year1990
Volume87
Pages5368-72
AuthorsDolan ME, Moschel RC, Pegg AE
TitleDepletion of mammalian O6-alkylguanine-DNA alkyltransferase activity by O6-benzylguanine provides a means to evaluate the role of this protein in protection against carcinogenic and therapeutic alkylating agents
[3]
PubMed ID8156986
JournalEMBO J
Year1994
Volume13
Pages1495-501
AuthorsMoore MH, Gulbis JM, Dodson EJ, Demple B, Moody PC
TitleCrystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli.
[4]
CommentsCHARACTERIZATION
PubMed ID8202360
JournalNucleic Acids Res
Year1994
Volume22
Pages1613-9
AuthorsLiem LK, Lim A, Li BF
TitleSpecificities of human, rat and E. coli O6-methylguanine-DNA methyltransferases towards the repair of O6-methyl and O6-ethylguanine in DNA.
Related Swiss-protP16455
[5]
PubMed ID8632775
JournalMutat Res
Year1996
Volume363
Pages15-25
AuthorsCrone TM, Goodtzova K, Pegg AE
TitleAmino acid residues affecting the activity and stability of human O6-alkylguanine-DNA alkyltransferase.
[6]
PubMed ID9403175
JournalChem Res Toxicol
Year1997
Volume10
Pages1234-9
AuthorsTerashima I, Kawate H, Sakumi K, Sekiguchi M, Kohda K
TitleSubstrate specificity of human O6-methylguanine-DNA methyltransferase for O6-benzylguanine derivatives in oligodeoxynucleotides
[7]
PubMed ID9757089
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages750-6
AuthorsCowtan K
TitleModified phased translation functions and their application to molecular-fragment location.
[8]
PubMed ID9445381
JournalBiochem J
Year1998
Volume329
Pages545-50
AuthorsKanugula S, Goodtzova K, Pegg AE
TitleProbing of conformational changes in human O6-alkylguanine-DNA alkyl transferase protein in its alkylated and DNA-bound states by limited proteolysis.
[9]
PubMed ID9730821
JournalBiochemistry
Year1998
Volume37
Pages12489-95
AuthorsGoodtzova K, Kanugula S, Edara S, Pegg AE
TitleInvestigation of the role of tyrosine-114 in the activity of human O6-alkylguanine-DNA alkyltranferase.
[10]
PubMed ID9556560
JournalJ Biol Chem
Year1998
Volume273
Pages10863-7
AuthorsPegg AE, Kanugula S, Edara S, Pauly GT, Moschel RC, Goodtzova K
TitleReaction of O6-benzylguanine-resistant mutants of human O6-alkylguanine-DNA alkyltransferase with O6-benzylguanine in oligodeoxyribonucleotides.
[11]
PubMed ID10346901
JournalBiochemistry
Year1999
Volume38
Pages6801-6
AuthorsSpratt TE, Wu JD, Levy DE, Kanugula S, Pegg AE
TitleReaction and binding of oligodeoxynucleotides containing analogues of O6-methylguanine with wild-type and mutant human O6-alkylguanine-DNA alkyltransferase.
[12]
PubMed ID10508414
JournalBiochemistry
Year1999
Volume38
Pages12097-103
AuthorsEncell LP, Loeb LA
TitleRedesigning the substrate specificity of human O(6)-alkylguanine-DNA alkyltransferase. Mutants with enhanced repair of O(4)-methylthymine.
[13]
CommentsX-ray crystallography
PubMed ID10747039
JournalEMBO J
Year2000
Volume19
Pages1719-30
AuthorsDaniels DS, Mol CD, Arvai AS, Kanugula S, Pegg AE, Tainer JA
TitleActive and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding.
Related PDB1eh6,1eh7,1eh8
[14]
PubMed ID10677686
JournalMutat Res
Year2000
Volume459
Pages81-7
AuthorsBrown LR, Deng J, Clarke ND
TitleDominant sensitization variants of human O(6)-methylguanine-DNA-methyltransferase obtained by a mutational screen of surface residues.
[15]
CommentsX-ray crystallography
PubMed ID10606635
JournalNucleic Acids Res
Year2000
Volume28
Pages393-401
AuthorsWibley JE, Pegg AE, Moody PC
TitleCrystal structure of the human O(6)-alkylguanine-DNA alkyltransferase.
Related PDB1qnt
[16]
PubMed ID11708909
JournalJ Med Chem
Year2001
Volume44
Pages4050-61
AuthorsReinhard J, Hull WE, von der Lieth CW, Eichhorn U, Kliem HC, Kaina B, Wiessler M
TitleMonosaccharide-linked inhibitors of O(6)-methylguanine-DNA methyltransferase (MGMT): synthesis, molecular modeling, and structure-activity relationships.
[17]
PubMed ID11983993
JournalActa Crystallogr C
Year2002
Volume58
Pageso284-6
AuthorsLow JN, Quesada A, Marchal A, Nogueras M, Sanchez A, Glidewell C
Title4-Amino-6-benzyloxy-2-(methylsulfanyl)-5-nitrosopyrimidine: hydrogen-bonded dimers linked into pi-stacked chains.
[18]
PubMed ID11983995
JournalActa Crystallogr C
Year2002
Volume58
Pageso289-94
AuthorsLow JN, Quesada A, Marchal A, Melguizo M, Nogueras M, Glidewell C
TitleHydrogen bonding in 2-amino-4,6-dimethoxypyrimidine, 2-benzylamino-4,6-bis(benzyloxy)pyrimidine and 2-amino-4,6-bis(N-pyrrolidino)pyrimidine: chains of fused rings and a centrosymmetric dimer.
[19]
PubMed ID12549918
JournalBiochemistry
Year2003
Volume42
Pages980-90
AuthorsRasimas JJ, Kanugula S, Dalessio PM, Ropson IJ, Fried MG, Pegg AE
TitleEffects of zinc occupancy on human O6-alkylguanine-DNA alkyltransferase.
[20]
PubMed ID12974631
JournalBiochemistry
Year2003
Volume42
Pages10965-70
AuthorsGuengerich FP, Fang Q, Liu L, Hachey DL, Pegg AE
TitleO6-alkylguanine-DNA alkyltransferase: low pKa and high reactivity of cysteine 145.

comments
According to the literature [3] & [13], the transfer of methyl group proceeds via SN2 mechanism as follows:
(1) A general base, His146, which is likely to be neutral, donating a hydrogen bond to carboxylate sidechain of Glu172, can abstract a proton from the thiolate group of Cys145, through a water molecule.
(2) Cys145 acts as a nucleophile, which attacks the methyl-group of O6-methylguanine.
(3) In addition, Tyr114 may protonate N3 atom of the guanine substrate as a general acid. According to another paper [11], Asn137 might stabilize the N1- and N2- positions of guanine.
Unique feature of this enzyme is that there is no acceptor substrate for the methyl group transferred to Cys145, which will not be removed. Therefore, the transfer reaction inactivates the enzyme, which will be rapidly degraded by proteases (see [13]).

createdupdated
2004-03-172009-02-26


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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