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

ABSTRACT: The aim of this study was to use comparative modeling to predict the three-dimensional structure of the CHAP(K) protein (cysteine, histidine-dependent amidohydrolase/peptidase domain of the LysK endolysin, derived from bacteriophage K). Iterative PSI-BLAST 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. A consensus Maximum Parsimony phylogenetic tree with a bootstrap analysis setting of 1,000 replicates was constructed using MEGA4. Structural templates relevant to our target (CHAP(K)) were identified, processed in Expresso and used to generate a 3D model in the alignment mode of SWISS-MODEL. These templates were also processed in the I-TASSER web server. A Staphylococcus

SUBMITTER: Fenton M 

PROVIDER: S-EPMC3448105 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature