DB code: D00077

RLCP classification	3.770.220000.47 : Transfer
CATH domain	2.30.37.60 : O6-alkylguanine-DNA Alkyltransferase; Chain A, domain 1
CATH domain	1.10.10.10 : Arc Repressor Mutant, subunit A	Catalytic domain
E.C.	2.1.1.63
CSA	1eh6
M-CSA	1eh6
MACiE	M0251

CATH domain	Related DB codes (homologues)
1.10.10.10 : Arc Repressor Mutant, subunit A	D00510 D00452 D00517 T00055 T00113

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	Pfam
P16455	Methylated-DNA--protein-cysteine methyltransferase	EC 2.1.1.63 6-O-methylguanine-DNA methyltransferase MGMT O-6-methylguanine-DNA-alkyltransferase	PF01035 (DNA_binding_1) PF02870 (Methyltransf_1N) [Graphical View]

KEGG enzyme name
methylated-DNA---[protein]-cysteine S-methyltransferase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P16455	MGMT_HUMAN	DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L- cysteine.		Nucleus.	Binds 1 zinc ion.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates		Products		Intermediates
KEGG-id	C04250	C02743	C00039	C03800
E.C.
Compound	DNA containing 6-O-methylguanine	Protein cysteine	DNA	Protein S-methyl-L-cysteine
Type	amine group,carbohydrate,nucleic acids	peptide/protein,sulfhydryl group	nucleic acids	peptide/protein,sulfide group
ChEBI
PubChem

1eh6A01	Unbound	Unbound	Unbound	Unbound
1eh7A01	Unbound	Unbound	Unbound	Unbound
1eh8A01	Unbound	Unbound	Unbound	Unbound
1qntA01	Unbound	Unbound	Unbound	Unbound
1eh6A02	Unbound	Unbound	Unbound	Unbound
1eh7A02	Unbound	Unbound	Unbound	Bound:SMC
1eh8A02	Unbound	Unbound	Unbound	Analogue:BCS
1qntA02	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
Swiss-prot;P16455 & literature

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1eh6A01
1eh7A01
1eh8A01
1qntA01
1eh6A02	TYR 114;ASN 137;CYS 145;HIS 146;GLU 172
1eh7A02	TYR 114;ASN 137;;HIS 146;GLU 172		SMC 145(methylated)
1eh8A02	TYR 114;ASN 137;;HIS 146;GLU 172		BCS 145(alkylated)
1qntA02	TYR 114;ASN 137;CYS 145;HIS 146;GLU 172

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	Figure 5, p.9319	1
[3]	Fig.3, p.1498, p.1499
[11]	Scheme 2, p.6805-6806
[13]	Fig.5, p.1727	1

References
[1]
Resource
Comments
Medline ID
PubMed ID	3174452
Journal	Nucleic Acids Res
Year	1988
Volume	16
Pages	9307-21
Authors	Yamagata Y, Kohda K, Tomita K
Title	Structural studies of O6-methyldeoxyguanosine and related compounds: a promutagenic DNA lesion by methylating carcinogens.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	2164681
Journal	Proc Natl Acad Sci U S A
Year	1990
Volume	87
Pages	5368-72
Authors	Dolan ME, Moschel RC, Pegg AE
Title	Depletion 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
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	8156986
Journal	EMBO J
Year	1994
Volume	13
Pages	1495-501
Authors	Moore MH, Gulbis JM, Dodson EJ, Demple B, Moody PC
Title	Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli.
Related PDB
Related UniProtKB
[4]
Resource
Comments	CHARACTERIZATION
Medline ID
PubMed ID	8202360
Journal	Nucleic Acids Res
Year	1994
Volume	22
Pages	1613-9
Authors	Liem LK, Lim A, Li BF
Title	Specificities of human, rat and E. coli O6-methylguanine-DNA methyltransferases towards the repair of O6-methyl and O6-ethylguanine in DNA.
Related PDB
Related UniProtKB	P16455
[5]
Resource
Comments
Medline ID
PubMed ID	8632775
Journal	Mutat Res
Year	1996
Volume	363
Pages	15-25
Authors	Crone TM, Goodtzova K, Pegg AE
Title	Amino acid residues affecting the activity and stability of human O6-alkylguanine-DNA alkyltransferase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	9403175
Journal	Chem Res Toxicol
Year	1997
Volume	10
Pages	1234-9
Authors	Terashima I, Kawate H, Sakumi K, Sekiguchi M, Kohda K
Title	Substrate specificity of human O6-methylguanine-DNA methyltransferase for O6-benzylguanine derivatives in oligodeoxynucleotides
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	9757089
Journal	Acta Crystallogr D Biol Crystallogr
Year	1998
Volume	54
Pages	750-6
Authors	Cowtan K
Title	Modified phased translation functions and their application to molecular-fragment location.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	9445381
Journal	Biochem J
Year	1998
Volume	329
Pages	545-50
Authors	Kanugula S, Goodtzova K, Pegg AE
Title	Probing of conformational changes in human O6-alkylguanine-DNA alkyl transferase protein in its alkylated and DNA-bound states by limited proteolysis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID	9730821
Journal	Biochemistry
Year	1998
Volume	37
Pages	12489-95
Authors	Goodtzova K, Kanugula S, Edara S, Pegg AE
Title	Investigation of the role of tyrosine-114 in the activity of human O6-alkylguanine-DNA alkyltranferase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID	9556560
Journal	J Biol Chem
Year	1998
Volume	273
Pages	10863-7
Authors	Pegg AE, Kanugula S, Edara S, Pauly GT, Moschel RC, Goodtzova K
Title	Reaction of O6-benzylguanine-resistant mutants of human O6-alkylguanine-DNA alkyltransferase with O6-benzylguanine in oligodeoxyribonucleotides.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	10346901
Journal	Biochemistry
Year	1999
Volume	38
Pages	6801-6
Authors	Spratt TE, Wu JD, Levy DE, Kanugula S, Pegg AE
Title	Reaction and binding of oligodeoxynucleotides containing analogues of O6-methylguanine with wild-type and mutant human O6-alkylguanine-DNA alkyltransferase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID	10508414
Journal	Biochemistry
Year	1999
Volume	38
Pages	12097-103
Authors	Encell LP, Loeb LA
Title	Redesigning the substrate specificity of human O(6)-alkylguanine-DNA alkyltransferase. Mutants with enhanced repair of O(4)-methylthymine.
Related PDB
Related UniProtKB
[13]
Resource
Comments	X-ray crystallography
Medline ID
PubMed ID	10747039
Journal	EMBO J
Year	2000
Volume	19
Pages	1719-30
Authors	Daniels DS, Mol CD, Arvai AS, Kanugula S, Pegg AE, Tainer JA
Title	Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding.
Related PDB	1eh6 1eh7 1eh8
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID	10677686
Journal	Mutat Res
Year	2000
Volume	459
Pages	81-7
Authors	Brown LR, Deng J, Clarke ND
Title	Dominant sensitization variants of human O(6)-methylguanine-DNA-methyltransferase obtained by a mutational screen of surface residues.
Related PDB
Related UniProtKB
[15]
Resource
Comments	X-ray crystallography
Medline ID
PubMed ID	10606635
Journal	Nucleic Acids Res
Year	2000
Volume	28
Pages	393-401
Authors	Wibley JE, Pegg AE, Moody PC
Title	Crystal structure of the human O(6)-alkylguanine-DNA alkyltransferase.
Related PDB	1qnt
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID	11708909
Journal	J Med Chem
Year	2001
Volume	44
Pages	4050-61
Authors	Reinhard J, Hull WE, von der Lieth CW, Eichhorn U, Kliem HC, Kaina B, Wiessler M
Title	Monosaccharide-linked inhibitors of O(6)-methylguanine-DNA methyltransferase (MGMT): synthesis, molecular modeling, and structure-activity relationships.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID	11983993
Journal	Acta Crystallogr C
Year	2002
Volume	58
Pages	o284-6
Authors	Low JN, Quesada A, Marchal A, Nogueras M, Sanchez A, Glidewell C
Title	4-Amino-6-benzyloxy-2-(methylsulfanyl)-5-nitrosopyrimidine: hydrogen-bonded dimers linked into pi-stacked chains.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID	11983995
Journal	Acta Crystallogr C
Year	2002
Volume	58
Pages	o289-94
Authors	Low JN, Quesada A, Marchal A, Melguizo M, Nogueras M, Glidewell C
Title	Hydrogen 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.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID	12549918
Journal	Biochemistry
Year	2003
Volume	42
Pages	980-90
Authors	Rasimas JJ, Kanugula S, Dalessio PM, Ropson IJ, Fried MG, Pegg AE
Title	Effects of zinc occupancy on human O6-alkylguanine-DNA alkyltransferase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID	12974631
Journal	Biochemistry
Year	2003
Volume	42
Pages	10965-70
Authors	Guengerich FP, Fang Q, Liu L, Hachey DL, Pegg AE
Title	O6-alkylguanine-DNA alkyltransferase: low pKa and high reactivity of cysteine 145.
Related PDB
Related UniProtKB

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]).

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]).

Created	Updated
2004-03-17	2009-02-26