期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 429, 期 24, 页码 3850-3862出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2017.10.022
关键词
DMSP; DMSP lyase DddY; DMS generation; cupin superfamily; catalytic mechanism
资金
- National Science Foundation of China [31630012, 31290231, 31290230, 31470541]
- National Key Research and Development Program of China [2016YFA0601303]
- Aoshan Talents Program
- Program of Shandong for Taishan Scholars [TS20090803]
- National Postdoctoral Program for Innovative Talents [BX201600095, BX201700145]
- NERC [NE/M004449/1, NE/P012671/1, NE/N002385/1] Funding Source: UKRI
The marine osmolyte dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Bacterial DMSP lyases cleave DMSP, producing acrylate and dimethyl sulfide (DMS), a climate-active gas with roles in global sulfur cycling and atmospheric chemistry. DddY is the only known periplasmic DMSP lyase and is present in beta-, gamma-, delta-and epsilon-proteobacteria. Unlike other known DMSP lyases, DddY has not been classified into a protein superfamily, and its structure and catalytic mechanism are unknown. Here, we determined the crystal structure of DddY from the y-proteobacterium Acinetobacter bereziniae originally isolated from human clinical specimens. This structure revealed that DddY contains a cap domain and a catalytic domain with a Zn (2+)bound at its active site. We also observed that the DddY catalytic domain adopts a typical p-barrel fold and contains two conserved cupin motifs. Therefore, we concluded that DddY should belong to the cupin superfamily. Using structural and mutational analyses, we identified key residues involved in Zn (2+)coordination, DMSP binding and the catalysis of DMSP cleavage, enabling elucidation of the catalytic mechanism, in which the residue Tyr271 of DddY acts as a general base to attack DMSP. Moreover, sequence analysis suggested that this proposed mechanism is common to DddY proteins from beta-, gamma-, delta-and e-proteobacteria. The DddY structure and proposed catalytic mechanism provide a better understanding of how DMSP is catabolized to generate the important climate-active gas DMS. (c) 2017 Elsevier Ltd. All rights reserved.
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