title: Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.
abstract: Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix α3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
authors.forename: Ashish
authors.initials: A
authors.lastname: Kabra
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.|Academy of Scientific and Innovative Research, New Delhi 110025, India.
authors.forename: Salman
authors.initials: S
authors.lastname: Shahid
authors.affiliation: X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India.
authors.forename: Ravi Kant
authors.initials: RK
authors.lastname: Pal
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Yadav
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
authors.forename: S V S Rama Krishna
authors.initials: SV
authors.lastname: Pulavarti
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
authors.forename: Anupam
authors.initials: A
authors.lastname: Jain
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
authors.forename: Sarita
authors.initials: S
authors.lastname: Tripathi
authors.affiliation: Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.|Academy of Scientific and Innovative Research, New Delhi 110025, India.
authors.forename: Ashish
authors.initials: A
authors.lastname: Arora
mesh_terms: D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055162:Biocatalysis; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004795:Enzyme Stability; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013816:Thermodynamics; D014734:Vibrio cholerae / Q000737:chemistry* / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D012346:RNA, Transfer, Amino Acyl; D011994:Recombinant Proteins; C019037:tRNA, peptidyl-; D002265:Carboxylic Ester Hydrolases; C019674:aminoacyl-tRNA hydrolase
keywords: MD simulations; catalytic mechanism; peptidyl-tRNA hydrolase; protein structure; relaxation dynamics; thermostability