5XKY

Crystal structure of DddY Se derivative

5XKY の概要

• エントリーDOI: 10.2210/pdb5xky/pdb
• 関連するPDBエントリー: 5XKX 5XKZ
• 分子名称: Uncharacterized protein, ZINC ION (3 entities in total)
• 機能のキーワード: dimethylsulfoniopropionate (dmsp) lyase, lyase
• 由来する生物種: Acinetobacter bereziniae NIPH 3
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 47382.03

構造登録者

Li, C.Y.,Zhang, Y.Z. (登録日: 2017-05-10, 公開日: 2017-11-01, 最終更新日: 2024-11-13)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.303 Å)