8HI4

Cryo-EM structure of the bi-functional malonyl-CoA reductase from Roseiflexus castenholzii

8HI4 の概要

• エントリーDOI: 10.2210/pdb8hi4/pdb
• EMDBエントリー: 34812
• 分子名称: Short-chain dehydrogenase/reductase SDR (1 entity in total)
• 機能のキーワード: the 3-hydroxypropionate cycle, bifunctional enzyme, short chain dehydrogenase, oxidoreductase
• 由来する生物種: Roseiflexus castenholzii DSM 13941
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 268536.75

構造登録者

Zhang, X.,Xu, X.,Xin, J. (登録日: 2022-11-18, 公開日: 2023-05-31, 最終更新日: 2023-09-20)

主引用文献

Zhang, X.,Xin, J.,Wang, Z.,Wu, W.,Liu, Y.,Min, Z.,Xin, Y.,Liu, B.,He, J.,Zhang, X.,Xu, X.
Structural basis of a bi-functional malonyl-CoA reductase (MCR) from the photosynthetic green non-sulfur bacterium Roseiflexus castenholzii.
Mbio, 14:e0323322-e0323322, 2023

PubMed Abstract: Malonyl-CoA reductase (MCR) is a NADPH-dependent bi-functional enzyme that performs alcohol dehydrogenase and aldehyde dehydrogenase (CoA-acylating) activities in the N- and C-terminal fragments, respectively. It catalyzes the two-step reduction of malonyl-CoA to 3-hydroxypropionate (3-HP), a key reaction in the autotrophic CO fixation cycles of green non-sulfur bacteria and the archaea . However, the structural basis underlying substrate selection, coordination, and the subsequent catalytic reactions of full-length MCR is largely unknown. For the first time, we here determined the structure of full-length MCR from the photosynthetic green non-sulfur bacterium (MCR) at 3.35 Å resolution. Furthermore, we determined the crystal structures of the N- and C-terminal fragments bound with reaction intermediates NADP and malonate semialdehyde (MSA) at 2.0 Å and 2.3 Å, respectively, and elucidated the catalytic mechanisms using a combination of molecular dynamics simulations and enzymatic analyses. Full-length MCR was a homodimer of two cross-interlocked subunits, each containing four tandemly arranged short-chain dehydrogenase/reductase (SDR) domains. Only the catalytic domains SDR1 and SDR3 incorporated additional secondary structures that changed with NADP-MSA binding. The substrate, malonyl-CoA, was immobilized in the substrate-binding pocket of SDR3 through coordination with Arg1164 and Arg799 of SDR4 and the extra domain, respectively. Malonyl-CoA was successively reduced through protonation by the Tyr743-Arg746 pair in SDR3 and the catalytic triad (Thr165-Tyr178-Lys182) in SDR1 after nucleophilic attack from NADPH hydrides. IMPORTANCE The bi-functional MCR catalyzes NADPH-dependent reduction of malonyl-CoA to 3-HP, an important metabolic intermediate and platform chemical, from biomass. The individual MCR-N and MCR-C fragments, which contain the alcohol dehydrogenase and aldehyde dehydrogenase (CoA-acylating) activities, respectively, have previously been structurally investigated and reconstructed into a malonyl-CoA pathway for the biosynthetic production of 3-HP. However, no structural information for full-length MCR has been available to illustrate the catalytic mechanism of this enzyme, which greatly limits our capacity to increase the 3-HP yield of recombinant strains. Here, we report the cryo-electron microscopy structure of full-length MCR for the first time and elucidate the mechanisms underlying substrate selection, coordination, and catalysis in the bi-functional MCR. These findings provide a structural and mechanistic basis for enzyme engineering and biosynthetic applications of the 3-HP carbon fixation pathways.

PubMed: 37278533
DOI: 10.1128/mbio.03233-22

実験手法

ELECTRON MICROSCOPY (3.35 Å)