Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis

Mycobacterium tuberculosis is a gram-positive bacterium causes tuberculosis in human. H37Rv strain is a pathogenic strain utilizedfor tuberculosis research. The cytidylate mono-phosphate (CMP) kinase of Mycobacterium tuberculosis belongs to the familynucleoside mono-phosphate kinase (NMK), this enzyme is required for the bacterial growth. Therefore, it is important to study thestructural and functional features of this enzyme in the control of the disease. Hence, we developed the structural molecular modelof the CMP kinase protein from Mycobacterium tuberculosis by homology modeling using the software MODELLER (9v10). Based onsequence similarity with protein of known structure (template) of Mycobacterium smegmatis (PDB ID: 3R20) was chosen fromprotein databank (PDB) by using BLASTp. The energy of constructed models was minimized and the qualities of the models wereevaluated by PROCHECK and VERRIFY-3D. Resulted Ramachandran plot analysis showed that conformations for 100.00% ofamino acids residues are within the most favored regions. A possible homologous deep cleft active site was identified in the Modelusing CASTp program. Amino acid composition and polarity of that protein was observed by CLC-Protein Workbench tool.Expasy''s Prot-param server and CYC_REC tool were used for physiochemical and functional characterization of the protein.Studied of secondary structure of that protein was carried out by computational program, ProFunc. The structure is finallysubmitted in Protein Model Database. The predicted model permits initial inferences about the unexplored 3D structure of theCMP kinase and may be promote in relational designing of molecules for structure-function studies.