EzCatDB: S00188
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00188
RLCP classification1.40.300.2 : Hydrolysis
CATH domainDomain 13.10.300.10 : 3-methyladenine DNA Glycosylase; Chain ACatalytic domain
E.C.3.2.2.21


Enzyme Name
UniProtKBKEGG

P29372
Protein nameDNA-3-methyladenine glycosylaseDNA-3-methyladenine glycosylase II
deoxyribonucleate 3-methyladenine glycosidase II
3-methyladenine DNA glycosylase II
DNA-3-methyladenine glycosidase II
AlkA
SynonymsEC 3.2.2.21
3-methyladenine DNA glycosidase
ADPG
3-alkyladenine DNA glycosylase
N-methylpurine-DNA glycosylase
RefSeqNP_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)
PfamPF02245 (Pur_DNA_glyco)
[Graphical view]


UniProtKB:Accession NumberP29372
Entry name3MG_HUMAN
ActivityHydrolysis of alkylated DNA, releasing 3- methyladenine, 3-methylguanine, 7-methylguanine and 7- methyladenine.
SubunitBinds MBD1.
Subcellular locationNucleus (Potential).
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00871C00001C00913C02230C02242C02241C02270
CompoundAlkylated DNAH2O3-Methyladenine3-Methylguanine7-Methylguanine7-MethyladenineBase-removed DNA
Typenucleic acidsH2Oamine 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
46893
46892
27564
46897
46894
28664
28921

PubChem
962
22247451
1673
76292
11361
71593

               
1bnkAUnbound UnboundUnboundUnboundUnboundAnalogue:G-A-C-A-T-G-YRR-T-T-G-C-C-T(chain D)
1ewnAAnalogue:G-A-C-A-T-G-EDA-T-T-G-C-C(chain D) UnboundUnboundUnboundUnboundUnbound
1f4rAAnalogue:G-A-C-A-T-G-EDA-T-T-G-C-C(chain D) UnboundUnboundUnboundUnboundUnbound
1f6oAUnbound UnboundUnboundUnboundUnboundAnalogue:G-A-C-A-T-G-YRR-T-T-G-C-C-T(chain D)

Active-site residues
resource
literature [3]
pdbCatalytic residuescomment
          
1bnkAGLU 125;ASP 132
 
1ewnA       ;ASP 132
mutant E125Q
1f4rAGLU 125;ASP 132
 
1f6oAGLU 125;ASP 132
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.1B1
[2]Fig.1B1
[3]p.251-252, Fig.4B1
[4]p.670-671
[5]p.4281-4282
[6]p.208
[7]p.13577-13578
[9]p.312

references
[1]
PubMed ID7806489
JournalJ Biol Chem
Year1994
Volume269
Pages32709-12
AuthorsDodson ML, Michaels ML, Lloyd RS
TitleUnified catalytic mechanism for DNA glycosylases.
[2]
PubMed ID7642635
JournalJ Biol Chem
Year1995
Volume270
Pages19501-8
AuthorsSun B, Latham KA, Dodson ML, Lloyd RS
TitleStudies on the catalytic mechanism of five DNA glycosylases. Probing for enzyme-DNA imino intermediates.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 80-199.
PubMed ID9790531
JournalCell
Year1998
Volume95
Pages249-58
AuthorsLau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T
TitleCrystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.
Related PDB1bnk
Related UniProtKBP29372
[4]
PubMed ID10440863
JournalBioessays
Year1999
Volume21
Pages668-76
AuthorsWyatt MD, Allan JM, Lau AY, Ellenberger TE, Samson LD
Title3-methyladenine DNA glycosylases: structure, function, and biological importance.
[5]
PubMed ID10660595
JournalJ Biol Chem
Year2000
Volume275
Pages4278-82
AuthorsRoy R, Biswas T, Lee JC, Mitra S
TitleMutation of a unique aspartate residue abolishes the catalytic activity but not substrate binding of the mouse N-methylpurine-DNA glycosylase (MPG).
[6]
PubMed ID10946229
JournalMutat Res
Year2000
Volume460
Pages201-10
AuthorsHollis T, Lau A, Ellenberger T
TitleStructural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase.
[7]
CommentsX-ray crystallography
PubMed ID11106395
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages13573-8
AuthorsLau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T
TitleMolecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.
Related PDB1f4r,1f6o,1ewn
[8]
PubMed ID11554308
JournalProg Nucleic Acid Res Mol Biol
Year2001
Volume68
Pages305-14
AuthorsHollis T, Lau A, Ellenberger T
TitleCrystallizing thoughts about DNA base excision repair.
[9]
PubMed ID11554309
JournalProg Nucleic Acid Res Mol Biol
Year2001
Volume68
Pages315-47
AuthorsHosfield DJ, Daniels DS, Mol CD, Putnam CD, Parikh SS, Tainer JA
TitleDNA damage recognition and repair pathway coordination revealed by the structural biochemistry of DNA repair enzymes.
[10]
PubMed ID12323378
JournalChem Biol
Year2002
Volume9
Pages1033-41
AuthorsConnor EE, Wyatt MD
TitleActive-site clashes prevent the human 3-methyladenine DNA glycosylase from improperly removing bases.
[11]
PubMed ID12202763
JournalNucleic Acids Res
Year2002
Volume30
Pages3778-87
AuthorsGuliaev AB, Hang B, Singer B
TitleStructural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N-glycosylase.

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].

createdupdated
2002-09-062009-03-24
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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.