DB code: D00077

RLCP classification 3.770.220000.47 : Transfer
CATH domain 2.30.37.60 : O6-alkylguanine-DNA Alkyltransferase; Chain A, domain 1
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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eh7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eh8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1qntA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eh6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eh7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:SMC
1eh8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:BCS
1qntA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eh7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eh8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qntA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eh6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 114;ASN 137;CYS 145;HIS 146;GLU 172
1eh7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 114;ASN 137;;HIS 146;GLU 172 SMC 145(methylated)
1eh8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 114;ASN 137;;HIS 146;GLU 172 BCS 145(alkylated)
1qntA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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]).

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