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Title: Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution

Abstract

The three-dimensional structure of the APE2540 protein from A. pernix K1 has been determined by the multiple anomalous dispersion method at 1.7 Å resolution. The structure includes two monomers in the asymmetric unit and shares structural similarity with the YbaK protein or cysteinyl-tRNA{sup Pro} deacylase from H. influenzae. The crystal structure of APE2540, the putative trans-editing enzyme ProX from Aeropyrum pernix K1, was determined in a high-throughput manner. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 Å, β = 106.8°. The structure was solved by the multiwavelength anomalous dispersion method at 1.7 Å and refined to an R factor of 16.8% (R{sub free} = 20.5%). The crystal structure includes two protein molecules in the asymmetric unit. Each monomer consists of eight β-strands and seven α-helices. A structure-homology search revealed similarity between the trans-editing enzyme YbaK (or cysteinyl-tRNA{sup Pro} deacylase) from Haemophilus influenzae (HI1434; 22% sequence identity) and putative ProX proteins from Caulobacter crescentus (16%) and Agrobacterium tumefaciens (21%)

Authors:
; ; ; ; ; ; ; ;  [1];  [1];  [2];  [1]
  1. RIKEN Genomic Sciences Center, Yokohama (Japan)
  2. RIKEN Harima Institute at SPring-8, Hyogo (Japan)
Publication Date:
OSTI Identifier:
22356077
Resource Type:
Journal Article
Journal Name:
Acta Crystallographica. Section F
Additional Journal Information:
Journal Volume: 61; Journal Issue: Pt 1; Other Information: PMCID: PMC1952386; PMID: 16508081; PUBLISHER-ID: gx5036; OAI: oai:pubmedcentral.nih.gov:1952386; Copyright (c) International Union of Crystallography 2005; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 1744-3091
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; CRYSTAL STRUCTURE; CRYSTALS; DISPERSIONS; MOLECULES; MONOMERS; R FACTORS; RESOLUTION; SPACE GROUPS

Citation Formats

Murayama, Kazutaka, Kato-Murayama, Miyuki, Katsura, Kazushige, Uchikubo-Kamo, Tomomi, Yamaguchi-Hirafuji, Machiko, Kawazoe, Masahito, Akasaka, Ryogo, Hanawa-Suetsugu, Kyoko, Hori-Takemoto, Chie, Terada, Takaho, RIKEN Harima Institute at SPring-8, Hyogo, Shirouzu, Mikako, Yokoyama, Shigeyuki, RIKEN Harima Institute at SPring-8, Hyogo, and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution. United Kingdom: N. p., 2005. Web. doi:10.1107/S1744309104032555.
Murayama, Kazutaka, Kato-Murayama, Miyuki, Katsura, Kazushige, Uchikubo-Kamo, Tomomi, Yamaguchi-Hirafuji, Machiko, Kawazoe, Masahito, Akasaka, Ryogo, Hanawa-Suetsugu, Kyoko, Hori-Takemoto, Chie, Terada, Takaho, RIKEN Harima Institute at SPring-8, Hyogo, Shirouzu, Mikako, Yokoyama, Shigeyuki, RIKEN Harima Institute at SPring-8, Hyogo, & Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution. United Kingdom. https://doi.org/10.1107/S1744309104032555
Murayama, Kazutaka, Kato-Murayama, Miyuki, Katsura, Kazushige, Uchikubo-Kamo, Tomomi, Yamaguchi-Hirafuji, Machiko, Kawazoe, Masahito, Akasaka, Ryogo, Hanawa-Suetsugu, Kyoko, Hori-Takemoto, Chie, Terada, Takaho, RIKEN Harima Institute at SPring-8, Hyogo, Shirouzu, Mikako, Yokoyama, Shigeyuki, RIKEN Harima Institute at SPring-8, Hyogo, and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo. 2005. "Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution". United Kingdom. https://doi.org/10.1107/S1744309104032555.
@article{osti_22356077,
title = {Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 Å resolution},
author = {Murayama, Kazutaka and Kato-Murayama, Miyuki and Katsura, Kazushige and Uchikubo-Kamo, Tomomi and Yamaguchi-Hirafuji, Machiko and Kawazoe, Masahito and Akasaka, Ryogo and Hanawa-Suetsugu, Kyoko and Hori-Takemoto, Chie and Terada, Takaho and RIKEN Harima Institute at SPring-8, Hyogo and Shirouzu, Mikako and Yokoyama, Shigeyuki and RIKEN Harima Institute at SPring-8, Hyogo and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo},
abstractNote = {The three-dimensional structure of the APE2540 protein from A. pernix K1 has been determined by the multiple anomalous dispersion method at 1.7 Å resolution. The structure includes two monomers in the asymmetric unit and shares structural similarity with the YbaK protein or cysteinyl-tRNA{sup Pro} deacylase from H. influenzae. The crystal structure of APE2540, the putative trans-editing enzyme ProX from Aeropyrum pernix K1, was determined in a high-throughput manner. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 Å, β = 106.8°. The structure was solved by the multiwavelength anomalous dispersion method at 1.7 Å and refined to an R factor of 16.8% (R{sub free} = 20.5%). The crystal structure includes two protein molecules in the asymmetric unit. Each monomer consists of eight β-strands and seven α-helices. A structure-homology search revealed similarity between the trans-editing enzyme YbaK (or cysteinyl-tRNA{sup Pro} deacylase) from Haemophilus influenzae (HI1434; 22% sequence identity) and putative ProX proteins from Caulobacter crescentus (16%) and Agrobacterium tumefaciens (21%)},
doi = {10.1107/S1744309104032555},
url = {https://www.osti.gov/biblio/22356077}, journal = {Acta Crystallographica. Section F},
issn = {1744-3091},
number = Pt 1,
volume = 61,
place = {United Kingdom},
year = {Sat Jan 01 00:00:00 EST 2005},
month = {Sat Jan 01 00:00:00 EST 2005}
}