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Title: Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation

Abstract

E. coli YfcM was expressed, purified and crystallized. Crystals of YfcM were obtained by the in situ proteolysis crystallization method. Using these crystals, an X-ray diffraction data set was collected at 1.45 Å resolution. Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (V{sub M}) of the crystal was 1.91 Å{sup 3} Da{sup −1}, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.

Authors:
 [1];  [2]; ;  [3];  [1];  [2];  [1]
  1. Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)
  2. (Japan)
  3. RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)
Publication Date:
OSTI Identifier:
22375704
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta crystallographica. Section F, Structural biology communications; Journal Volume: 70; Journal Issue: Pt 9; Other Information: PMCID: PMC4157426; PMID: 25195899; PUBLISHER-ID: us5058; OAI: oai:pubmedcentral.nih.gov:4157426; Copyright (c) Kobayashi et al. 2014; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; CRYSTALLIZATION; CRYSTALS; ELONGATION; ESCHERICHIA COLI; LYSINE; MODIFICATIONS; MOLECULES; PROTEINS; RESOLUTION; SOLVENTS; SPACE GROUPS; X-RAY DIFFRACTION

Citation Formats

Kobayashi, Kan, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Suzuki, Takehiro, Dohmae, Naoshi, Ishitani, Ryuichiro, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, and Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp. Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation. United States: N. p., 2014. Web. doi:10.1107/S2053230X14015726.
Kobayashi, Kan, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Suzuki, Takehiro, Dohmae, Naoshi, Ishitani, Ryuichiro, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, & Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp. Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation. United States. doi:10.1107/S2053230X14015726.
Kobayashi, Kan, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Suzuki, Takehiro, Dohmae, Naoshi, Ishitani, Ryuichiro, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, and Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp. Wed . "Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation". United States. doi:10.1107/S2053230X14015726.
@article{osti_22375704,
title = {Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation},
author = {Kobayashi, Kan and RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 and Suzuki, Takehiro and Dohmae, Naoshi and Ishitani, Ryuichiro and RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 and Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp},
abstractNote = {E. coli YfcM was expressed, purified and crystallized. Crystals of YfcM were obtained by the in situ proteolysis crystallization method. Using these crystals, an X-ray diffraction data set was collected at 1.45 Å resolution. Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (V{sub M}) of the crystal was 1.91 Å{sup 3} Da{sup −1}, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.},
doi = {10.1107/S2053230X14015726},
journal = {Acta crystallographica. Section F, Structural biology communications},
number = Pt 9,
volume = 70,
place = {United States},
year = {Wed Aug 27 00:00:00 EDT 2014},
month = {Wed Aug 27 00:00:00 EDT 2014}
}
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