From Protein Structure to Function with Bioinformatics.pdf

10 Integrated Servers for Structure-Informed Function Prediction 261abcFig. 10.5 The closest fold to that of 2fck, found by the SSM fold-matching program, is PDBentry 1s7f, a RimL N(α)-acetyltransferase from Salmonella typhimurium. (a) Overall 3D structureof 2fck and (b) overall structure of 1s7f in the same orientation. (c) The two structure superposedand each shown as a Cα trace, 2fck in yellow and 1s7f in purple. The matched regions are shownusing a thicker representation of the trace in each structurelarge trough capable of binding the N-terminal helices of L12. The protein alsobinds coenzyme A (coA) some distance away from the substrate binding site.10.3.1.2 Helix-Turn-Helix (HTH) DNA-Binding MotifsThe second of the structure-based methods is a search for any helix-turn-helix(HTH) motifs which match a database of such motifs extracted from PDB structuresknown to be involved in DNA binding (Jones et al. 2003; Aravind et al. 2005).False positives are filtered out using parameters based on a combination of solvent