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

Journal Article · Wed Aug 27 04:00:00 EDT 2014 · Acta crystallographica. Section F, Structural biology communications

DOI:https://doi.org/10.1107/S2053230X14015726· OSTI ID:22375704

Kobayashi, Kan ^[1]; Suzuki, Takehiro; Dohmae, Naoshi ^[2]; Ishitani, Ryuichiro ^[1]; Nureki, Osamu ^[1]

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1. Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)
2. RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

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%.

• OSTI ID: 22375704
• Journal Information: Acta crystallographica. Section F, Structural biology communications, Journal Name: Acta crystallographica. Section F, Structural biology communications Journal Issue: Pt 9 Vol. 70; ISSN ACSFEN; ISSN 2053-230X
• Country of Publication: United States
• Language: English

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
CRYSTALLIZATION
CRYSTALS
ELONGATION
ESCHERICHIA COLI
LYSINE
MODIFICATIONS
MOLECULES
PROTEINS
RESOLUTION
SOLVENTS
SPACE GROUPS
X-RAY DIFFRACTION