DB code: S00749

RLCP classification 1.40.7050.132 : Hydrolysis
CATH domain 1.10.340.30 : Endonuclease III; domain 1 Catalytic domain
E.C. 3.2.2.20
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P05100 DNA-3-methyladenine glycosylase 1
EC 3.2.2.20
3-methyladenine-DNA glycosylase I, constitutive
TAG I
DNA-3-methyladenine glycosidase I
DNA-3-methyladenine glycosylase I
NP_418005.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491887.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF03352 (Adenine_glyco)
[Graphical View]
Q8Z2A5
3-methyladenine DNA glycosylase I
3-methyladenine DNA glycosylase I, constitutive
NP_807495.1 (Protein)
NC_004631.1 (DNA/RNA sequence)
PF03352 (Adenine_glyco)
[Graphical View]
Q9RL93
DNA-3-methyladenine glycosidase
PF03352 (Adenine_glyco)
[Graphical View]

KEGG enzyme name
DNA-3-methyladenine glycosylase I
Deoxyribonucleate 3-methyladenine glycosidase I
3-methyladenine DNA glycosylase I
DNA-3-methyladenine glycosidase I

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P05100 3MG1_ECOLI Hydrolysis of alkylated DNA, releasing 3-methyladenine.
Q8Z2A5 Q8Z2A5_SALTI
Q9RL93 Q9RL93_STAAU

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00871 C00001 C00913 C02270
E.C.
Compound Zinc Alkylated DNA H2O 3-Methyladenine Base-removed DNA
Type heavy metal nucleic acids H2O amine group,aromatic ring (with nitrogen atoms) carbohydrate,nucleic acids,phosphate group/phosphate ion
ChEBI 29105
15377
38635
PubChem 32051
22247451
962
1673
1lmzA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1nkuA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound
1p7mA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Bound:ADK Unbound
2ofiA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Bound:ADK Bound:C-G-G-A-C-T-3DR-A-C-G-G-G (chain B)
2ofkA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound
2ofkB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound
2jg6A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Literature [2], [4], [5], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1lmzA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
1nkuA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
1p7mA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2ofiA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2ofkA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2ofkB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)
2jg6A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 16;GLU 38;TRP 46 CYS 4;HIS 17;HIS 175;CYS 179 (Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.7, p.48019
[7]
Figure 4

References
[1]
Resource
Comments
Medline ID
PubMed ID 12509243
Journal DNA Repair (Amst)
Year 2002
Volume 1
Pages 391-5
Authors Bujnicki JM, Rychlewski L
Title Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases.
Related PDB
Related UniProtKB
[2]
Resource
Comments STRUCTURE BY NMR.
Medline ID
PubMed ID 12161745
Journal Nat Struct Biol
Year 2002
Volume 9
Pages 659-64
Authors Drohat AC, Kwon K, Krosky DJ, Stivers JT
Title 3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Related PDB 1lmz
Related UniProtKB P05100
[3]
Resource
Comments
Medline ID
PubMed ID 12848584
Journal Chem Rev
Year 2003
Volume 103
Pages 2729-59
Authors Stivers JT, Jiang YL
Title A mechanistic perspective on the chemistry of DNA repair glycosylases.
Related PDB
Related UniProtKB
[4]
Resource
Comments STRUCTURE BY NMR IN COMPLEX WITH 3-METHYLADENINE, ZINC-BINDING SITES.
Medline ID
PubMed ID 13129925
Journal J Biol Chem
Year 2003
Volume 278
Pages 48012-20
Authors Cao C, Kwon K, Jiang YL, Drohat AC, Stivers JT
Title Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I.
Related PDB 1p7m
Related UniProtKB P05100
[5]
Resource
Comments STRUCTURE BY NMR, ZINC-BINDING SITES.
Medline ID
PubMed ID 12654914
Journal J Biol Chem
Year 2003
Volume 278
Pages 19442-6
Authors Kwon K, Cao C, Stivers JT
Title A novel zinc snap motif conveys structural stability to 3-methyladenine DNA glycosylase I.
Related PDB 1nku
Related UniProtKB P05100
[6]
Resource
Comments
Medline ID
PubMed ID 15102448
Journal Curr Opin Struct Biol
Year 2004
Volume 14
Pages 43-9
Authors Fromme JC, Banerjee A, Verdine GL
Title DNA glycosylase recognition and catalysis.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 17410210
Journal EMBO J
Year 2007
Volume 26
Pages 2411-20
Authors Metz AH, Hollis T, Eichman BF
Title DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
Related PDB 2ofi 2ofk
Related UniProtKB Q8Z2A5
[8]
Resource
Comments
Medline ID
PubMed ID 19659577
Journal FEMS Microbiol Rev
Year 2009
Volume 33
Pages 1044-78
Authors Dalhus B, Laerdahl JK, Backe PH, Bjoras M
Title DNA base repair--recognition and initiation of catalysis.
Related PDB
Related UniProtKB

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.

Created Updated
2010-07-22 2011-10-07