title: Mutational analysis of Mycobacterium tuberculosis lysine ɛ-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes.
abstract: Lysine ɛ-aminotransferase (LAT) converts lysine to α-aminoadipate-δ-semialdehyde in a PLP-mediated reaction. We mutated active-site T330, N328 and E243, and structurally rationalized their properties. T330A and T330S mutants cannot bind PLP and are inactive. N328A although inactive, binds to PLP. E243A retains activity, but binds α-ketoglutarate in a different conformation. We had earlier identified 2-aminomethyl piperidine derivative as a LAT inhibitor. The co-crystal structure reveals that it mimics binding of C5 substrates and exhibits two binding modes. E243, that shields R422 in the apo enzyme, exhibits conformational changes to permit the binding of the inhibitor in one of the binding modes. Structure-based analysis of bound water in the active site suggests optimization strategies for synthesis of improved inhibitors.
authors.affiliation: Molecular & Structural Biology Division, Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India.
authors.forename: Sarvind Mani
authors.initials: SM
authors.lastname: Tripathi
authors.affiliation: Molecular & Structural Biology Division, Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India.
authors.forename: Aparna
authors.initials: A
authors.lastname: Agarwal
authors.affiliation: Molecular & Structural Biology Division, Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India. Electronic address: r_ravishankar@cdri.res.in.
authors.forename: Ravishankar
authors.initials: R
authors.lastname: Ramachandran
mesh_terms: D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics*; D020134:Catalytic Domain / Q000235:genetics; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D007656:Ketoglutaric Acids / Q000378:metabolism; D051306:L-Lysine 6-Transaminase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics*; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009169:Mycobacterium tuberculosis / Q000201:enzymology* / Q000235:genetics*; D010880:Piperidines / Q000737:chemistry / Q000494:pharmacology; D011487:Protein Conformation; D011732:Pyridoxal Phosphate / Q000378:metabolism; D055672:Static Electricity
chemical_list: D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D007656:Ketoglutaric Acids; D010880:Piperidines; D011732:Pyridoxal Phosphate; D051306:L-Lysine 6-Transaminase
keywords: 2-Aminomethyl piperidine derivative; Crystal structure; Glu243 switch; Lysine ε-aminotransferase; Mycobacterium tuberculosis; α-ketoglutarate