EzCatDB: S00749
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DB codeS00749
RLCP classification1.40.7050.132 : Hydrolysis
CATH domainDomain 11.10.340.30 : Endonuclease III; domain 1Catalytic domain
E.C.3.2.2.20
CSA1p7m

CATH domainRelated DB codes (homologues)
1.10.340.30 : Endonuclease III; domain 1D00511,T00070,D00266

Enzyme Name
UniProtKBKEGG

P05100Q8Z2A5Q9RL93
Protein nameDNA-3-methyladenine glycosylase 1

DNA-3-methyladenine glycosylase I
Deoxyribonucleate 3-methyladenine glycosidase I
3-methyladenine DNA glycosylase I
DNA-3-methyladenine glycosidase I
SynonymsEC 3.2.2.20
DNA-3-methyladenine glycosylase I
3-methyladenine-DNA glycosylase I, constitutive
TAG I
DNA-3-methyladenine glycosidase I
3-methyladenine DNA glycosylase I, constitutive
3-methyladenine DNA glycosylase I
DNA-3-methyladenine glycosidase
RefSeqNP_418005.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491887.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_807495.1 (Protein)
NC_004631.1 (DNA/RNA sequence)

PfamPF03352 (Adenine_glyco)
[Graphical view]
PF03352 (Adenine_glyco)
[Graphical view]
PF03352 (Adenine_glyco)
[Graphical view]


UniProtKB:Accession NumberP05100Q8Z2A5Q9RL93
Entry name3MG1_ECOLIQ8Z2A5_SALTIQ9RL93_STAAU
ActivityHydrolysis of alkylated DNA, releasing 3-methyladenine.

Subunit


Subcellular location


Cofactor



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C00871C00001C00913C02270
CompoundZincAlkylated DNAH2O3-MethyladenineBase-removed DNA
Typeheavy metalnucleic acidsH2Oamine group,aromatic ring (with nitrogen atoms)carbohydrate,nucleic acids,phosphate group/phosphate ion
ChEBI29105

15377
38635

PubChem32051

962
22247451
1673

             
1lmzA00UnboundUnbound UnboundUnbound
1nkuA00Bound:_ZNUnbound UnboundUnbound
1p7mA00Bound:_ZNUnbound Bound:ADKUnbound
2ofiA00Bound:_ZNUnbound Bound:ADKBound:C-G-G-A-C-T-3DR-A-C-G-G-G(chain B)
2ofkA00Bound:_ZNUnbound UnboundUnbound
2ofkB00Bound:_ZNUnbound UnboundUnbound
2jg6A00Bound:_ZNUnbound UnboundUnbound

Active-site residues
resource
Literature [2], [4], [5], [7]
pdbCatalytic residuesCofactor-binding residues
          
1lmzA00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
1nkuA00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
1p7mA00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2ofiA00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2ofkA00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2ofkB00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2jg6A00TYR 16;GLU 38;TRP 46
CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Fig.7, p.48019
[7]Figure 4

references
[1]
PubMed ID12509243
JournalDNA Repair (Amst)
Year2002
Volume1
Pages391-5
AuthorsBujnicki JM, Rychlewski L
TitleFold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases.
[2]
CommentsSTRUCTURE BY NMR.
PubMed ID12161745
JournalNat Struct Biol
Year2002
Volume9
Pages659-64
AuthorsDrohat AC, Kwon K, Krosky DJ, Stivers JT
Title3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Related PDB1lmz
Related UniProtKBP05100
[3]
PubMed ID12848584
JournalChem Rev
Year2003
Volume103
Pages2729-59
AuthorsStivers JT, Jiang YL
TitleA mechanistic perspective on the chemistry of DNA repair glycosylases.
[4]
CommentsSTRUCTURE BY NMR IN COMPLEX WITH 3-METHYLADENINE, ZINC-BINDING SITES.
PubMed ID13129925
JournalJ Biol Chem
Year2003
Volume278
Pages48012-20
AuthorsCao C, Kwon K, Jiang YL, Drohat AC, Stivers JT
TitleSolution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I.
Related PDB1p7m
Related UniProtKBP05100
[5]
CommentsSTRUCTURE BY NMR, ZINC-BINDING SITES.
PubMed ID12654914
JournalJ Biol Chem
Year2003
Volume278
Pages19442-6
AuthorsKwon K, Cao C, Stivers JT
TitleA novel zinc snap motif conveys structural stability to 3-methyladenine DNA glycosylase I.
Related PDB1nku
Related UniProtKBP05100
[6]
PubMed ID15102448
JournalCurr Opin Struct Biol
Year2004
Volume14
Pages43-9
AuthorsFromme JC, Banerjee A, Verdine GL
TitleDNA glycosylase recognition and catalysis.
[7]
PubMed ID17410210
JournalEMBO J
Year2007
Volume26
Pages2411-20
AuthorsMetz AH, Hollis T, Eichman BF
TitleDNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
Related PDB2ofi,2ofk
Related UniProtKBQ8Z2A5
[8]
PubMed ID19659577
JournalFEMS Microbiol Rev
Year2009
Volume33
Pages1044-78
AuthorsDalhus B, Laerdahl JK, Backe PH, Bjoras M
TitleDNA base repair--recognition and initiation of catalysis.

comments
Although zinc ion is included as a cofactor, it is not involved in catalysis. Zinc must stabilize the domain structure (see [5]).
This enzyme is homologous to AlkA glycosylase (T00070 in EzCatDB). However, its active site is different from that of the homologous enzyme.
According to the literature [2], [3], [4] and [7], this enzyme catalyzes the following reaction:
(0) Glu38 hydrogen-bonds to N6 and N7 of 3-methyladenine (3-MeA) and Tyr16 hydrogen-bonds to N1, whereas Trp46 makes a pi-pi stacking with 3-MeA. Thus, these residues indirectly stabilize the oxocarbenium-like transition-state by interacting with the base. (The positive charge may develop on C1' atom of DNA-deoxyribose.)
(1) A water may makes a nucleophilic attack on the C1' atom of DNA-deoxyribose, to complete reaction.

createdupdated
2010-07-222011-10-07


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 - )
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