4S00

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP mutant Y366A in complex with acrylate

Summary for 4S00

• Entry DOI: 10.2210/pdb4s00/pdb
• Descriptor: Peptidase M24, FE (III) ION, ACRYLIC ACID, ... (5 entities in total)
• Functional Keywords: metallopeptidase-like, dmsp lyase, lyase
• Biological source: Silicibacter lacuscaerulensis ITI-1157
• Total number of polymer chains: 4
• Total formula weight: 202959.83

Authors

Zhang, Y.,Wang, P. (deposition date: 2014-12-27, release date: 2015-08-05, Last modification date: 2024-02-28)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.099 Å)