4LA3

Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ Y131A in complex with DMSP

4LA3 の概要

• エントリーDOI: 10.2210/pdb4la3/pdb
• 関連するPDBエントリー: 4LA2
• 分子名称: Dimethylsulphoniopropionate (DMSP) lyase DddQ, ZINC ION, 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid, ... (4 entities in total)
• 機能のキーワード: cupin motif, dmsp lyase, lyase
• 由来する生物種: Silicibacter lacuscaerulensis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 44262.11

構造登録者

Zhang, Y.,Li, C. (登録日: 2013-06-19, 公開日: 2014-01-15, 最終更新日: 2023-11-08)

主引用文献

Li, C.,Wei, T.,Zhang, S.,Chen, X.,Gao, X.,Wang, P.,Xie, B.,Su, H.,Qin, Q.,Zhang, X.,Yu, J.,Zhang, H.,Zhou, B.,Yang, G.,Zhang, Y.
Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide
Proc.Natl.Acad.Sci.USA, 111:1026-1031, 2014

PubMed Abstract: The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn(2+) ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.

PubMed: 24395783
DOI: 10.1073/pnas.1312354111

実験手法

X-RAY DIFFRACTION (2.701 Å)