5MTE

Crystal structure of PDF from the Vibrio parahaemolyticus bacteriophage VP16T in complex with actinonin - crystal form II

5MTE の概要

• エントリーDOI: 10.2210/pdb5mte/pdb
• 分子名称: Putative uncharacterized protein orf60T, ACTINONIN, ZINC ION, ... (5 entities in total)
• 機能のキーワード: pdf, peptide deformylase, type 1b, bacteriophage vp16t, actinonin, 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: 30686.44

構造登録者

Fieulaine, S.,Grzela, R.,Giglione, C.,Meinnel, T. (登録日: 2017-01-09, 公開日: 2017-11-29, 最終更新日: 2024-10-16)

主引用文献

Grzela, R.,Nusbaum, J.,Fieulaine, S.,Lavecchia, F.,Desmadril, M.,Nhiri, N.,Van Dorsselaer, A.,Cianferani, S.,Jacquet, E.,Meinnel, T.,Giglione, C.
Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts.
Biochim. Biophys. Acta, 1866:348-355, 2018

PubMed Abstract: Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.

PubMed: 29101077
DOI: 10.1016/j.bbapap.2017.10.007

実験手法

X-RAY DIFFRACTION (1.4 Å)