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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1diz

E.C. nameDNA-3-methyladenine glycosylase II
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 3.2.2.21
CSA Homologues of 1dizThere are 10 Homologs
CSA Entries With UniProtID P04395
CSA Entries With EC Number 3.2.2.21
PDBe Entry 1diz
PDBSum Entry 1diz
MACiE Entry M0313

Literature Report

IntroductionA variety of environmental toxins can react with DNA and chemically alkylate the bases. This blocks the replicative polymerases and interferes with binding of regulatory proteins to DNA resulting in widespread cellular responses including activation of cell cycle checkpoints and programmed cell death. There are a number of repair strategies - direct reversal, nucleotide excision repair and base excision repair. Most single base modifications are corrected using base excision repair. Firstly a lesion specific DNA glycosylase removes the damaged base by hydrolysis of the deoxyribose glycosidic bond of alkylated DNA. The abasic site is then excised and filled by DNA polymerase.
MechansimThe bound DNA is highly distorted. This is achieved by surprisingly few contacts. Lys170 interacts with the DNA phosphate backbone. The active site cleft is flanked by a wedge tipped with Leu125 which juts into the minor groove and displaces the base targeted for excision. It also causes a 66 degree bend in the DNA away from the protein which disrupts base pair stacking interactions either side of the flipped out base. At the base of the wedge Pro175 is forced into the minor groove and makes Van der Waals contacts with the deoxyribose sugar leading to a two fold expansion of the minor groove. The DNA is tightly anchored to the protein by a series of hydrogen bonds and metal mediated interaction by residues 202 to 227. Gly214, Gly216 and Thr219 are involved in hydrogen bonding whilst the main chain carbonyl atoms of Gln210, Phe212 and Ile215 along with the phosphate oxygen of the DNA backbone and a water molecule coordinate a metal ion, thought to be sodium. The active site cleft is lined with electron rich aromatic rings from Phe18, Trp218, Tyr222, Trp272 and Tyr273 which form strong pi-donor/acceptor interactions with the electron deficient substrate, stabilising the extrahelical conformation of the alkylated base. Although the reaction could proceed via an Sn2 mechanism the lack of space present for a water nucleophile suggests an Sn1 type reaction. The positive nature of the substrate means that they do not require a general acid to protonate them. The carboxylate group of Asp238 stabilises the carbocation intermediate by ionic and covalent interactions leading to the release of the alkylated base. Since there is no suitably placed general acid this explains the selectivity for positive modified bases.

Catalytic Sites for 1diz

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
TrpA272272macie:sideChain
AspA238238macie:sideChain
TyrA222222macie:sideChain

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
TrpB272272macie:sideChain
AspB238238macie:sideChain
TyrB222222macie:sideChain

Literature References

Notes:
Hollis T
Structural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase.
Mutat Res 2000 460 201-210
PubMed: 10946229
Hollis T
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
EMBO J 2000 19 758-766
PubMed: 10675345
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