5XKY

Crystal structure of DddY Se derivative

Summary for 5XKY

• Entry DOI: 10.2210/pdb5xky/pdb
• Related: 5XKX 5XKZ
• Descriptor: Uncharacterized protein, ZINC ION (3 entities in total)
• Functional Keywords: dimethylsulfoniopropionate (dmsp) lyase, lyase
• Biological source: Acinetobacter bereziniae NIPH 3
• Total number of polymer chains: 1
• Total formula weight: 47382.03

Authors

Li, C.Y.,Zhang, Y.Z. (deposition date: 2017-05-10, release date: 2017-11-01, Last modification date: 2018-01-24)

Primary citation

Li, C.Y.,Zhang, D.,Chen, X.L.,Wang, P.,Shi, W.L.,Li, P.Y.,Zhang, X.Y.,Qin, Q.L.,Todd, J.D.,Zhang, Y.Z.
Mechanistic Insights into Dimethylsulfoniopropionate Lyase DddY, a New Member of the Cupin Superfamily.
J. Mol. Biol., 429:3850-3862, 2017

PubMed Abstract: 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 β-, γ-, δ- and ε-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 γ-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 bound at its active site. We also observed that the DddY catalytic domain adopts a typical β-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 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 β-, γ-, δ- and ε-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.

PubMed: 29106934
DOI: 10.1016/j.jmb.2017.10.022

Experimental method

X-RAY DIFFRACTION (2.303 Å)