In silico modeling of the staphylococcal bacteriophage-derived peptidase CHAP sub(K)

The aim of this study was to use comparative modeling to predict the three-dimensional structure of the CHAP[subK] protein (cysteine, histidine dependent amidohydrolase/peptidase domain of the LysK endolysin, derived from bacteriophage K). Iterative PSI-BLAS T searches against the Protein Data Bank (PDB) and nonredundant (nr) databases were used to populate a multiple alignment for analysis using the T-Coffee Expresso server. Structural templates relevant to our target (CHAP [subK]) were identified, processed in Expresso and used to generate a 3D model in the alignment mode of SWISS-MODEL. Use of comparative modeling has allowed approximation of the 3D structure of CHAP[subK] giving information on the structure and an insight into the binding and active site of the catalytic domain. This may facilitate its development as an alternative antibacterial agent.