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
38635
27564
46892
46893
28664
46894
46897
28921
PubChem 22247451
962
1673
76292
11361
71593
1bnkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:G-A-C-A-T-G-YRR-T-T-G-C-C-T (chain D)
1ewnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:G-A-C-A-T-G-EDA-T-T-G-C-C (chain D) Unbound Unbound Unbound Unbound Unbound
1f4rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:G-A-C-A-T-G-EDA-T-T-G-C-C (chain D) Unbound Unbound Unbound Unbound Unbound
1f6oA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 125;ASP 132
1ewnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 132 mutant E125Q
1f4rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 125;ASP 132
1f6oA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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].

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