AlkA_N

AlkA N-terminal domain
AlkA_N
SMART accession number:SM01009
Description: This domain is found at the N terminus of bacterial AlkA . AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove (PUBMED:10675345).
Interpro abstract (IPR010316):

This domain is found at the N terminus of bacterial AlkA EC 3.2.2.21. AlkA (DNA-3-methyladenine glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove [(PUBMED:10675345)].

This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision [(PUBMED:8706136)]. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [(PUBMED:12009927)].

Family alignment:
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There are 422 AlkA_N domains in 422 proteins in SMART's nrdb database.

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