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Overview for MACiE Entry M0313

Version history

General Information

EC Number: 3.2.2.21 (A member of the Hydrolases, Glycosylases, Hydrolysing N-glycosyl compounds)

Enzyme Name: DNA-3-methyladenine glycosylase II

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P04395 - DNA-3-methyladenine glycosylase 2

Representative PDB Code: 1diz - CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNAGLYCOSYLASE (ALKA) COMPLEXED WITH DNA (Resolution = 2.50 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of 3-methyladenine DNA

Image of water

right arrow

Image of DNA minus adenine base

Image of 3-methyladenine

3-methyladenine DNA
X00140
water
C00001
CHEBI:15377
DNA minus adenine base
X00141
3-methyladenine
C00913
CHEBI:1590

Overall Comment: AlkA lacks an obvious residue that could fulfill the role of a general acid to protonate the leaving group and later activate a water molecule. It is thought that AlkA's positively charged, alkylated substrates might not require this type of assistance. The lack of a general acid in AlkA's active site provides a means of catalytic selectivity. Positively charged bases, which do not require protonation and have a weakened glycosylic bond, can be removed effectively, and in turn it may function as a general base to activate a nearby water molecule. Unmodified bases require protonation by a general acid prior to hydrolysis and therefore are poor substrates. [3]


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Stepwise Description of the Reaction

Step 1The DNA substrate undergoes heterolysis, eliminating the alkylated base.
Step 2The eliminated base deprotonates water, which adds to the DNA.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Asp 228 A Side Chain
Tyr 222 A Side Chain

References

  1. T. Hollis et al. (2000), Mutat. Res., 460, 201-210. Structural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase.
    Medline: 10946229
  2. J. Labahn et al. (0), Cell, 86, 321-329. .
    Medline: 8706136
  3. T. Hollis et al. (2000), The EMBO Journal, 19, 758-766. DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
    Medline: 10675345

Homologue information for M0313 (1diz)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0185 DNA-(apurinic or apyrimidinic site) lyase
4.2.99.18
1lwy 1.10.340.30
0.20370.2999Compare

Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

GOA logo
DNA binding (molecular function)
catalytic activity (molecular function)
alkylbase DNA N-glycosylase activity (molecular function)
DNA repair (biological process)
base-excision repair (biological process)
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