Homology modeling

Homology models were constructed for M. tuberculosis cytidylate kinase, Rv1712, using Modeller version 9.7 [38]. Homologous template structures were identified by amino-acid sequence alignment against those of the Protein Data Bank (PDB) [39] using the profile.build module of Modeller. Multiple sequence alignments were obtained using the salign routine. The manually optimized alignment was used by Modeller model-mult-hetero module to construct the models based on satisfaction of spatial restraints. Structural templates for Rv1712 were cytidine monophosphate kinase (CMPK) from Streptococcus pneumoniae (1Q3T), cytidylate kinase from Staphylococcus aureus in complex with cytidine-5-monophosphate (2H92), and CMPK from E. coli both without (1CKE) and with C5P (1KDO). We randomly generated fifty models for Rv1712 using Modeller in the presence of ligand C5P.