4s00

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

spinqualitylabelsall models 4s00, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4s00 is a 4 chain structure with sequence from Ruegeria lacuscaerulensis ITI-1157. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: AKR, FE, GOL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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. 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.,Wang P, Chen XL, Li CY, Gao X, Zhu DY, Xie BB, Qin QL, Zhang XY, Su HN, Zhou BC, Xun LY, Zhang YZ Mol Microbiol. 2015 Jul 8. doi: 10.1111/mmi.13119. PMID:26154071 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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