4S01

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP mutant D377N in complex with acrylate

4S01 の概要

• エントリーDOI: 10.2210/pdb4s01/pdb
• 分子名称: Peptidase M24, FE (III) ION, ACRYLIC ACID, ... (5 entities in total)
• 機能のキーワード: metallopeptidase-like dmsp lyase, dmsp lyase, lyase
• 由来する生物種: Silicibacter lacuscaerulensis ITI-1157
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 202955.89

構造登録者

Zhang, Y.,Wang, P. (登録日: 2014-12-27, 公開日: 2015-08-05, 最終更新日: 2024-02-28)

主引用文献

Wang, P.,Chen, X.L.,Li, C.Y.,Gao, X.,Zhu, D.Y.,Xie, B.B.,Qin, Q.L.,Zhang, X.Y.,Su, H.N.,Zhou, B.C.,Xun, L.Y.,Zhang, Y.Z.
Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.
Mol.Microbiol., 98:289-301, 2015

PubMed Abstract: The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria, and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds, but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO4 (3-) and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Furthermore, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production.

PubMed: 26154071
DOI: 10.1111/mmi.13119

実験手法

X-RAY DIFFRACTION (2.1 Å)