Computational protocol: Mycobacterium tuberculosis Phosphoribosylpyrophosphate Synthetase: Biochemical Features of a Crucial Enzyme for Mycobacterial Cell Wall Biosynthesis

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Protocol publication

[…] The three dimensional structure of MtbPRPPase was modelled using, as the template, the atomic coordinates of the X-ray crystal structure of the human ortholog in complex with AMP, cadmium and sulfate ion (PDB code 2HCR) . The program SWISS-PDBviewer in conjunction with the SWISS-MODEL server (http://www.expasy.org/spdbv/) was employed for building and optimizing the model. The stereochemistry of the predicted structure has been assessed with the program PROCHECK . 92.0% of residues felt in the most favoured region of the Ramachandran plot, 8.0% in the additional allowed region with no detected outliers. The crystal structure of human PRPPase and the modelled MtbPRPPase structure can be superimposed with a r.m.s.d. of 0.5 Å based on 303 Ca pairs (the two enzymes share a sequence identity of 44%). The model of the MtbPRPPase-AMP complex was obtained by superposing the predicted M. tuberculosis structure onto the crystal structure of human template and pasting the AMP molecule into the M. tuberculosis modelled structure. Figures were generated with the program Pymol . […]

Pipeline specifications

Software tools Swiss-PdbViewer, SWISS-MODEL, PROCHECK, PyMOL
Databases ExPASy
Applications Small-angle scattering, Protein structure analysis
Organisms Mycobacterium tuberculosis
Diseases Tuberculosis, Tuberculosis, Multidrug-Resistant, Extensively Drug-Resistant Tuberculosis
Chemicals Adenosine Diphosphate, Adenosine Triphosphate, Guanosine Diphosphate, Nucleotides, Phosphoribosyl Pyrophosphate