title: A homology model of the three-dimensional structure of human O6-alkylguanine-DNA alkyltransferase based on the crystal structure of the C-terminal domain of the Ada protein from Escherichia coli.
abstract: O6-Alkylguanine-DNA alkyltransferase (EC 2.1.1.63) repairs O6-alkylguanine lesions in DNA. A homology model of the human protein (hAT) was built, based on the crystal structure of the C-terminal domain of the Ada protein, which carries out a similar repair in Escherichia coli. Sequence alignments of known O6-alkylguanine-DNA alkyltransferases were used to aid the model building using QUANTA and CHARMm software. Despite low homology in the N-terminal half (hAT residues 1-85), a well-defined topology over this region in Ada permitted successful modelling. The C-terminal half of hAT (residues 92-207) was modelled almost entirely by residue-for-residue superposition onto the Ada structure up to residue hAT175. The model was solvated to a residue radius of 8.0 A [corrected] and then minimized using CHARMm. This structural model was used to rationalize findings from site-directed mutagenesis experiments on hAT, to make further predictions on the relationship between structure and function for the alkyltransferase family of proteins, and to explain the specificity towards known small-molecule inhibitors of the protein.
authors.affiliation: Department of Pharmacy, University of Manchester, UK.
authors.forename: J E
authors.initials: JE
authors.lastname: Wibley
authors.forename: J H
authors.initials: JH
authors.lastname: McKie
authors.forename: K
authors.initials: K
authors.lastname: Embrey
authors.forename: D S
authors.initials: DS
authors.lastname: Marks
authors.forename: K T
authors.initials: KT
authors.lastname: Douglas
authors.forename: M H
authors.initials: MH
authors.lastname: Moore
authors.forename: P C
authors.initials: PC
authors.lastname: Moody
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D029968:Escherichia coli Proteins; D006801:Humans; D008780:Methyltransferases / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019853:O(6)-Methylguanine-DNA Methyltransferase; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D012984:Software; D013237:Stereoisomerism; D014157:Transcription Factors
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D014157:Transcription Factors; D008780:Methyltransferases; C045675:Ada protein, E coli; D019853:O(6)-Methylguanine-DNA Methyltransferase