From Protein Structure to Function with Bioinformatics.pdf

266 R.A. LaskowskiGly97Gly99Tyr98Tyr100Leu116Leu114abcFig. 10.7 A reverse template match between 2fck and 1s7f, a RimL N(α)-acetyltransferase fromSalmonella typhimurium. (a) The yellow residues are the template residues from 2fck (Gly99,Tyr100 and Leu116) which match to the purple residues (Gly97, Tyr98 and Leu114, respectively)in 1s7f with an RMSD of 0.62 Å for 17 matched atoms. (b) The equivalent residues of identicaltype within 10 Å of the template centre. There are 16 residues in all (out of 44 within 10 Å) givinga local similarity of 36.4%. A further 20 superposed residues (not shown) are of similar type (e.g.Ile for Val). (c) Sequence alignment obtained from the structural superposition. The top row showsthe secondary structure of 2fck and the bottom shows that of 1s7f; any helices are represented bythe jagged elements and β-strands by arrows. The three highlighted residues in the sequence alignmentcorrespond to the template residues. Double dots between the two sequences identify theresidues contained within the 10 Å sphere centred on the template and hence show which residueswere used to drive the alignment. The boxed regions represent segments of the alignment wherethe sequence identity of the two sequences exceeds 35%. The long thin arrows at the bottom showstructurally “fittable” regions; that is, segments from both proteins whose Cα atoms can be structurallysuperposed with an RMSD of less than 3.0 ÅAlso quoted is the overall structural similarity of the structures and the longeststretch of the two sequences that superposes with an root-mean-square deviation(RMSD) of 3.0 Å on the Cα atoms. This latter can be particularly revealing whenthere is a long overlap, suggesting a significant structural match, even for the longshot cases.