5MTD

Crystal structure of PDF from the Vibrio parahaemolyticus bacteriophage VP16T - crystal form II

5MTD の概要

• エントリーDOI: 10.2210/pdb5mtd/pdb
• 分子名称: Putative uncharacterized protein orf60T, TRIETHYLENE GLYCOL, ZINC ION, ... (5 entities in total)
• 機能のキーワード: pdf, peptide deformylase, type 1b, bacteriophage vp16t, hydrolase
• 由来する生物種: Vibrio phage VP16T
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 30215.80

構造登録者

Fieulaine, S.,Grzela, R.,Giglione, C.,Meinnel, T. (登録日: 2017-01-09, 公開日: 2017-09-20, 最終更新日: 2024-01-17)

主引用文献

Grzela, R.,Nusbaum, J.,Fieulaine, S.,Lavecchia, F.,Bienvenut, W.V.,Dian, C.,Meinnel, T.,Giglione, C.
The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation.
Sci Rep, 7:11041-11041, 2017

PubMed Abstract: Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.

PubMed: 28887476
DOI: 10.1038/s41598-017-11329-3

実験手法

X-RAY DIFFRACTION (1.5 Å)