DB code: S00188

RLCP classification	1.40.300.2 : Hydrolysis
CATH domain	3.10.300.10 : 3-methyladenine DNA Glycosylase; Chain A	Catalytic domain
E.C.	3.2.2.21
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P29372	DNA-3-methyladenine glycosylase	EC 3.2.2.21 3-methyladenine DNA glycosidase ADPG 3-alkyladenine DNA glycosylase N-methylpurine-DNA glycosylase	NP_001015052.1 (Protein) NM_001015052.2 (DNA/RNA sequence) NP_001015054.1 (Protein) NM_001015054.2 (DNA/RNA sequence) NP_002425.2 (Protein) NM_002434.3 (DNA/RNA sequence)	PF02245 (Pur_DNA_glyco) [Graphical View]

KEGG enzyme name
DNA-3-methyladenine glycosylase II deoxyribonucleate 3-methyladenine glycosidase II 3-methyladenine DNA glycosylase II DNA-3-methyladenine glycosidase II AlkA

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P29372	3MG_HUMAN	Hydrolysis of alkylated DNA, releasing 3- methyladenine, 3-methylguanine, 7-methylguanine and 7- methyladenine.	Binds MBD1.	Nucleus (Potential).

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates		Products					Intermediates
KEGG-id	C00871	C00001	C00913	C02230	C02242	C02241	C02270
E.C.
Compound	Alkylated DNA	H2O	3-Methyladenine	3-Methylguanine	7-Methylguanine	7-Methyladenine	Base-removed DNA
Type	nucleic acids	H2O	amine group,aromatic ring (with nitrogen atoms)	amine group,aromatic ring (with nitrogen atoms)	amide group,amine group,aromatic ring (with nitrogen atoms)	amine group,aromatic ring (with nitrogen atoms)	carbohydrate,nucleic acids,phosphate group/phosphate ion
ChEBI		15377 15377	38635 38635	27564 46892 46893 27564 46892 46893	28664 46894 46897 28664 46894 46897	28921 28921
PubChem		22247451 962 22247451 962	1673 1673	76292 76292	11361 11361	71593 71593

1bnkA	Unbound		Unbound	Unbound	Unbound	Unbound	Analogue:G-A-C-A-T-G-YRR-T-T-G-C-C-T (chain D)
1ewnA	Analogue:G-A-C-A-T-G-EDA-T-T-G-C-C (chain D)		Unbound	Unbound	Unbound	Unbound	Unbound
1f4rA	Analogue:G-A-C-A-T-G-EDA-T-T-G-C-C (chain D)		Unbound	Unbound	Unbound	Unbound	Unbound
1f6oA	Unbound		Unbound	Unbound	Unbound	Unbound	Analogue:G-A-C-A-T-G-YRR-T-T-G-C-C-T (chain D)

Reference for Active-site residues
resource	references	E.C.
literature [3]

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

1bnkA	GLU 125;ASP 132
1ewnA	;ASP 132				mutant E125Q
1f4rA	GLU 125;ASP 132
1f6oA	GLU 125;ASP 132

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	Fig.1B	1
[2]	Fig.1B	1
[3]	p.251-252, Fig.4B	1
[4]	p.670-671
[5]	p.4281-4282
[6]	p.208
[7]	p.13577-13578
[9]	p.312

References
[1]
Resource
Comments
Medline ID
PubMed ID	7806489
Journal	J Biol Chem
Year	1994
Volume	269
Pages	32709-12
Authors	Dodson ML, Michaels ML, Lloyd RS
Title	Unified catalytic mechanism for DNA glycosylases.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	7642635
Journal	J Biol Chem
Year	1995
Volume	270
Pages	19501-8
Authors	Sun B, Latham KA, Dodson ML, Lloyd RS
Title	Studies on the catalytic mechanism of five DNA glycosylases. Probing for enzyme-DNA imino intermediates.
Related PDB
Related UniProtKB
[3]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 80-199.
Medline ID
PubMed ID	9790531
Journal	Cell
Year	1998
Volume	95
Pages	249-58
Authors	Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T
Title	Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.
Related PDB	1bnk
Related UniProtKB	P29372
[4]
Resource
Comments
Medline ID
PubMed ID	10440863
Journal	Bioessays
Year	1999
Volume	21
Pages	668-76
Authors	Wyatt MD, Allan JM, Lau AY, Ellenberger TE, Samson LD
Title	3-methyladenine DNA glycosylases: structure, function, and biological importance.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	10660595
Journal	J Biol Chem
Year	2000
Volume	275
Pages	4278-82
Authors	Roy R, Biswas T, Lee JC, Mitra S
Title	Mutation of a unique aspartate residue abolishes the catalytic activity but not substrate binding of the mouse N-methylpurine-DNA glycosylase (MPG).
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	10946229
Journal	Mutat Res
Year	2000
Volume	460
Pages	201-10
Authors	Hollis T, Lau A, Ellenberger T
Title	Structural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase.
Related PDB
Related UniProtKB
[7]
Resource
Comments	X-ray crystallography
Medline ID
PubMed ID	11106395
Journal	Proc Natl Acad Sci U S A
Year	2000
Volume	97
Pages	13573-8
Authors	Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T
Title	Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.
Related PDB	1f4r 1f6o 1ewn
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	11554308
Journal	Prog Nucleic Acid Res Mol Biol
Year	2001
Volume	68
Pages	305-14
Authors	Hollis T, Lau A, Ellenberger T
Title	Crystallizing thoughts about DNA base excision repair.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID	11554309
Journal	Prog Nucleic Acid Res Mol Biol
Year	2001
Volume	68
Pages	315-47
Authors	Hosfield DJ, Daniels DS, Mol CD, Putnam CD, Parikh SS, Tainer JA
Title	DNA damage recognition and repair pathway coordination revealed by the structural biochemistry of DNA repair enzymes.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID	12323378
Journal	Chem Biol
Year	2002
Volume	9
Pages	1033-41
Authors	Connor EE, Wyatt MD
Title	Active-site clashes prevent the human 3-methyladenine DNA glycosylase from improperly removing bases.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	12202763
Journal	Nucleic Acids Res
Year	2002
Volume	30
Pages	3778-87
Authors	Guliaev AB, Hang B, Singer B
Title	Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N-glycosylase.
Related PDB
Related UniProtKB

Comments
By analogy to the cleavage of polysaccharides by glycosidases and N-glycosidic bonds in nucleosides by nucleoside hydrolase, the hydrolysis of N-glycosylic bonds by DNA glycosylases is likely to involve a transition state with considerable oxocarbenium ion character [3]. According to the paper [3], the bound water molecule is the nucleophile that is activated by nearby amino acids. The bound water is nearly aligned for attack of the N-glycosylic bond with subsequent release of the N-alkylated base via a backside displacement mechanism. O4' of a 2'-deoxyribonucleoside substrate would not attract the water, enabling its alignment for attack of the anomeric carbon. Glu125 could act as a general base, deprotonating the water for nucleophilic attack of the sugar [3]. According to the paper [5], Asp132 plays an essential role either by donating a proton to the substrate base and, thus, facilitating its release, or by stabilizing the steric configuration of the active site pocket. However, this aspartate residue, Asp132, is too distant from the substrate for the proton donation [5]. The papers, [6] & [9], reported that Glu125 might deprotonate the water, which is ideally positioned for an in-line displacement of the glycosidic bond via a backside attack of the ribose, to form a strong nucleophile that could then attack the C1' of the substrate ribose and subsequently release the base. The literature [7] suggested that some alkylation-damaged bases are electron deficient and have a delocalized positive charge, enabling the alkylated bases to be recognized by tight-binding ineractions with ana aromatic side chains of the glycosylase active site, which would constitute a pi-electron donor-acceptor pair with considerably more potential binding energy than a neutral pi-electron stacking interaction. Another feature is that a positively charged alkylated base is a good leaving group with a weakened glycosidic bond. With minimal catalytic assistance, these destabilized bases could be readily excised by a glycosylase lacking the catalytic strength to efficiently excise normal bases [7].

Comments

By analogy to the cleavage of polysaccharides by glycosidases and N-glycosidic bonds in nucleosides by nucleoside hydrolase, the hydrolysis of N-glycosylic bonds by DNA glycosylases is likely to involve a transition state with considerable oxocarbenium ion character [3]. According to the paper [3], the bound water molecule is the nucleophile that is activated by nearby amino acids. The bound water is nearly aligned for attack of the N-glycosylic bond with subsequent release of the N-alkylated base via a backside displacement mechanism. O4' of a 2'-deoxyribonucleoside substrate would not attract the water, enabling its alignment for attack of the anomeric carbon. Glu125 could act as a general base, deprotonating the water for nucleophilic attack of the sugar [3].
According to the paper [5], Asp132 plays an essential role either by donating a proton to the substrate base and, thus, facilitating its release, or by stabilizing the steric configuration of the active site pocket. However, this aspartate residue, Asp132, is too distant from the substrate for the proton donation [5].
The papers, [6] & [9], reported that Glu125 might deprotonate the water, which is ideally positioned for an in-line displacement of the glycosidic bond via a backside attack of the ribose, to form a strong nucleophile that could then attack the C1' of the substrate ribose and subsequently release the base.
The literature [7] suggested that some alkylation-damaged bases are electron deficient and have a delocalized positive charge, enabling the alkylated bases to be recognized by tight-binding ineractions with ana aromatic side chains of the glycosylase active site, which would constitute a pi-electron donor-acceptor pair with considerably more potential binding energy than a neutral pi-electron stacking interaction. Another feature is that a positively charged alkylated base is a good leaving group with a weakened glycosidic bond. With minimal catalytic assistance, these destabilized bases could be readily excised by a glycosylase lacking the catalytic strength to efficiently excise normal bases [7].

Created	Updated
2002-09-06	2009-03-24