دورية أكاديمية
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Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae.

التفاصيل البيبلوغرافية
العنوان: Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae.
المؤلفون: Mundra S; Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Department of Science and Technology, New Delhi 110016, India., Pal RK; X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India., Tripathi S; Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India., Jain A; Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India., Arora A; Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. Electronic address: ashish_arora@cdri.res.in.
المصدر: Biochimica et biophysica acta. Proteins and proteomics [Biochim Biophys Acta Proteins Proteom] 2021 Jan; Vol. 1869 (1), pp. 140554. Date of Electronic Publication: 2020 Oct 15.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101731734 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-1454 (Electronic) Linking ISSN: 15709639 NLM ISO Abbreviation: Biochim Biophys Acta Proteins Proteom Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Amsterdam : Elsevier
مواضيع طبية MeSH: Bacterial Proteins/*chemistry , Carboxylic Ester Hydrolases/*chemistry , Klebsiella pneumoniae/*enzymology , RNA, Transfer, Lys/*chemistry, Amino Acid Sequence ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Boron Compounds/chemistry ; Carboxylic Ester Hydrolases/genetics ; Carboxylic Ester Hydrolases/metabolism ; Catalytic Domain ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Kinetics ; Klebsiella pneumoniae/chemistry ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; RNA, Transfer, Lys/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity
مستخلص: Klebsiella pneumoniae is a member of the ESKAPE panel of pathogens that are top priority to tackle AMR. Bacterial peptidyl tRNA hydrolase (Pth), an essential, ubiquitous enzyme, hydrolyzes the peptidyl-tRNAs that accumulate in the cytoplasm because of premature termination of translation. Pth cleaves the ester bond between 2' or 3' hydroxyl of the ribose in the tRNA and C-terminal carboxylate of the peptide, thereby making free tRNA available for repeated cycles of protein synthesis and preventing cell death by alleviating tRNA starvation. Pth structures have been determined in peptide-bound or peptide-free states. In peptide-bound state, highly conserved residues F67, N69 and N115 adopt a conformation that is conducive to their interaction with peptide moiety of the substrate. While, in peptide-free state, these residues move away from the catalytic center, perhaps, in order to facilitate release of hydrolysed peptide. Here, we present a novel X-ray crystal structure of Pth from Klebsiella pneumoniae (KpPth), at 1.89 Å resolution, in which out of the two molecules in the asymmetric unit, one reflects the peptide-bound while the other reflects peptide-free conformation of the conserved catalytic site residues. Each molecule of the protein has canonical structure with seven stranded β-sheet structure surrounded by six α-helices. MD simulations indicate that both the forms converge over 500 ns simulation to structures with wider opening of the crevice at peptide-binding end. In solution, KpPth is monomeric and its 2D-HSQC spectrum displays a single set of well dispersed peaks. Further, KpPth was demonstrated to be enzymatically active on BODIPY-Lys-tRNA Lys3 .
(Copyright © 2020 Elsevier B.V. All rights reserved.)
فهرسة مساهمة: Keywords: Differential scanning calorimetry; Molecular dynamics simulation; NMR spectroscopy; Peptidyl-tRNA hydrolase; X-ray crystallography
المشرفين على المادة: 0 (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene)
0 (Bacterial Proteins)
0 (Boron Compounds)
0 (RNA, Transfer, Lys)
0 (Recombinant Proteins)
EC 3.1.1.- (Carboxylic Ester Hydrolases)
EC 3.1.1.29 (aminoacyl-tRNA hydrolase)
تواريخ الأحداث: Date Created: 20201017 Date Completed: 20210415 Latest Revision: 20210415
رمز التحديث: 20221213
DOI: 10.1016/j.bbapap.2020.140554
PMID: 33068756
قاعدة البيانات: MEDLINE
الوصف
تدمد:1878-1454
DOI:10.1016/j.bbapap.2020.140554