The essential process of protein biosynthesis in the cell often gets stalled due to the premature abortion of the translation process and generates a byproduct of peptidyl-tRNA molecules. This defect is corrected by peptidyl-tRNA hydrolase (Pth) by hydrolyzing peptidyl-tRNA to yield tRNA and peptides. In order to understand the mechanism of catalytic action and detailed stereochemical features of the substrate binding site, the structure of Pth has been determined at 1.00 Å resolution. The Pth enzyme from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized. The structure was refined to Rcryst and Rfree values of 0.145 and 0.157 respectively. The electron densities were observed for many hydrogen atoms in the structure. In AbPth, the residues, Asn12, His22, Asn70, Asp95 and Asn116 are involved in the catalytic process. The structure determination revealed that His22 Nᵟ1 forms a hydrogen bond with Asp95 Oᵟ2 while His22 Nε2 is hydrogen bonded to Asn116 Nᵟ2. In this case, the side chain of Asn116 adopts a conformation with value of 65°. Upon ligand binding, Asn116 adopts a different conformation with value of -70⁰. In the present structure, the conformation of Tyr68 is observed in the disallowed region of Ramachandran’s plot with φ, ѱ values of 80⁰, 150⁰. However, it is observed that Tyr68 adopts both disallowed and allowed conformations in Pth enzymes indicating a structural flexibility. The structure determination also revealed multiple conformations of the side chains of a number of amino acid residues.
| Published in | European Journal of Biophysics (Volume 9, Issue 1) |
| DOI | 10.11648/j.ejb.20210901.13 |
| Page(s) | 13-23 |
| Creative Commons |
This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
| Copyright |
Copyright © The Author(s), 2024. Published by Science Publishing Group |
Peptidyl-tRNA Hydrolase, Crystal Structure, Atomic Resolution, Catalytic Site, Protonation
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APA Style
Vijayan Viswanathan, Pradeep Sharma, Prashant Kumar Singh, Punit Kaur, Sujata Sharma, et al. (2021). Crystal Structure of Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.00 Å Resolution. European Journal of Biophysics, 9(1), 13-23. https://doi.org/10.11648/j.ejb.20210901.13
ACS Style
Vijayan Viswanathan; Pradeep Sharma; Prashant Kumar Singh; Punit Kaur; Sujata Sharma, et al. Crystal Structure of Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.00 Å Resolution. Eur. J. Biophys. 2021, 9(1), 13-23. doi: 10.11648/j.ejb.20210901.13
AMA Style
Vijayan Viswanathan, Pradeep Sharma, Prashant Kumar Singh, Punit Kaur, Sujata Sharma, et al. Crystal Structure of Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.00 Å Resolution. Eur J Biophys. 2021;9(1):13-23. doi: 10.11648/j.ejb.20210901.13
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Download@article{10.11648/j.ejb.20210901.13,
author = {Vijayan Viswanathan and Pradeep Sharma and Prashant Kumar Singh and Punit Kaur and Sujata Sharma and Tej Pal Singh},
title = {Crystal Structure of Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.00 Å Resolution},
journal = {European Journal of Biophysics},
volume = {9},
number = {1},
pages = {13-23},
doi = {10.11648/j.ejb.20210901.13},
url = {https://doi.org/10.11648/j.ejb.20210901.13},
eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejb.20210901.13},
abstract = {The essential process of protein biosynthesis in the cell often gets stalled due to the premature abortion of the translation process and generates a byproduct of peptidyl-tRNA molecules. This defect is corrected by peptidyl-tRNA hydrolase (Pth) by hydrolyzing peptidyl-tRNA to yield tRNA and peptides. In order to understand the mechanism of catalytic action and detailed stereochemical features of the substrate binding site, the structure of Pth has been determined at 1.00 Å resolution. The Pth enzyme from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized. The structure was refined to Rcryst and Rfree values of 0.145 and 0.157 respectively. The electron densities were observed for many hydrogen atoms in the structure. In AbPth, the residues, Asn12, His22, Asn70, Asp95 and Asn116 are involved in the catalytic process. The structure determination revealed that His22 Nᵟ1 forms a hydrogen bond with Asp95 Oᵟ2 while His22 Nε2 is hydrogen bonded to Asn116 Nᵟ2. In this case, the side chain of Asn116 adopts a conformation with value of 65°. Upon ligand binding, Asn116 adopts a different conformation with value of -70⁰. In the present structure, the conformation of Tyr68 is observed in the disallowed region of Ramachandran’s plot with φ, ѱ values of 80⁰, 150⁰. However, it is observed that Tyr68 adopts both disallowed and allowed conformations in Pth enzymes indicating a structural flexibility. The structure determination also revealed multiple conformations of the side chains of a number of amino acid residues.},
year = {2021}
}
TY - JOUR T1 - Crystal Structure of Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.00 Å Resolution AU - Vijayan Viswanathan AU - Pradeep Sharma AU - Prashant Kumar Singh AU - Punit Kaur AU - Sujata Sharma AU - Tej Pal Singh Y1 - 2021/03/17 PY - 2021 N1 - https://doi.org/10.11648/j.ejb.20210901.13 DO - 10.11648/j.ejb.20210901.13 T2 - European Journal of Biophysics JF - European Journal of Biophysics JO - European Journal of Biophysics SP - 13 EP - 23 PB - Science Publishing Group SN - 2329-1737 UR - https://doi.org/10.11648/j.ejb.20210901.13 AB - The essential process of protein biosynthesis in the cell often gets stalled due to the premature abortion of the translation process and generates a byproduct of peptidyl-tRNA molecules. This defect is corrected by peptidyl-tRNA hydrolase (Pth) by hydrolyzing peptidyl-tRNA to yield tRNA and peptides. In order to understand the mechanism of catalytic action and detailed stereochemical features of the substrate binding site, the structure of Pth has been determined at 1.00 Å resolution. The Pth enzyme from Acinetobacter baumannii (AbPth) was cloned, expressed, purified and crystallized. The structure was refined to Rcryst and Rfree values of 0.145 and 0.157 respectively. The electron densities were observed for many hydrogen atoms in the structure. In AbPth, the residues, Asn12, His22, Asn70, Asp95 and Asn116 are involved in the catalytic process. The structure determination revealed that His22 Nᵟ1 forms a hydrogen bond with Asp95 Oᵟ2 while His22 Nε2 is hydrogen bonded to Asn116 Nᵟ2. In this case, the side chain of Asn116 adopts a conformation with value of 65°. Upon ligand binding, Asn116 adopts a different conformation with value of -70⁰. In the present structure, the conformation of Tyr68 is observed in the disallowed region of Ramachandran’s plot with φ, ѱ values of 80⁰, 150⁰. However, it is observed that Tyr68 adopts both disallowed and allowed conformations in Pth enzymes indicating a structural flexibility. The structure determination also revealed multiple conformations of the side chains of a number of amino acid residues. VL - 9 IS - 1 ER -
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