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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
Author(s) -
Wang Peng,
Chen XiuLan,
Li ChunYang,
Gao Xiang,
Zhu Deyu,
Xie BinBin,
Qin QiLong,
Zhang XiYing,
Su HaiNan,
Zhou BaiCheng,
Xun Luying,
Zhang YuZhong
Publication year - 2015
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.13119
Subject(s) - dimethylsulfoniopropionate , lyase , biochemistry , biology , enzyme , catabolism , mutant , gene , ecology , phytoplankton , nutrient
Summary 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 ddd P gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M 24 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 Rl DddP (the DddP from R uegeria lacuscaerulensis ITI _1157) bound to inhibitory 2‐( N ‐morpholino) ethanesulfonic acid or PO 4 3− and of two mutants of Rl DddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion‐shift catalytic mechanism of Rl DddP 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.