8QWC

Cryo-EM structure of Apo coproheme decarboxylase from Corynebacterium diphtheria.

8QWC の概要

• エントリーDOI: 10.2210/pdb8qwc/pdb
• EMDBエントリー: 18688
• 分子名称: Coproheme decarboxylase (2 entities in total)
• 機能のキーワード: heme binding protein, heme biosynthesis, actinobacteria, oxidoreductase
• 由来する生物種: Corynebacterium diphtheriae
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 136444.80

構造登録者

Patil, G.,Guo, Y.,Borek, D.,Hofbauer, S. (登録日: 2023-10-19, 公開日: 2025-02-05)

主引用文献

Patil, G.,Alonso de Armino, D.J.,Guo, Y.,Furtmuller, P.G.,Borek, D.,Estrin, D.A.,Hofbauer, S.
Insights into the flexibility of the domain-linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations.
Protein Sci., 34:e70027-e70027, 2025

PubMed Abstract: Prokaryotic heme biosynthesis in Gram-positive bacteria follows the coproporphyrin-dependent heme biosynthesis pathway. The last step in this pathway is catalyzed by the enzyme coproheme decarboxylase, which oxidatively transforms two propionate groups into vinyl groups yielding heme b. The catalytic reaction cycle of coproheme decarboxylases exhibits four different states: the apo-form, the substrate (coproheme)-bound form, a transient three-propionate intermediate form (monovinyl, monopropionate deuteroheme; MMD), and the product (heme b)-bound form. In this study, we used cryogenic electron microscopy single-particle reconstruction (cryo-EM SPR) to characterize structurally the apo and heme b-bound forms of actinobacterial coproheme decarboxylase from Corynebacterium diphtheriae. The flexible loop that connects the N-terminal and the C-terminal ferredoxin domains of coproheme decarboxylases plays an important role in interactions between the enzyme and porphyrin molecule. To understand the role of this flexible loop, we performed molecular dynamics simulations on the apo and heme b coproheme decarboxylase from Corynebacterium diphtheriae. Our results are discussed in the context of the published structural information on coproheme-bound and MMD-bound coproheme decarboxylase and with respect to the reaction mechanism. Having structural information of all four enzymatically relevant states helps in understanding structural restraints with a functional impact.

PubMed: 39865384
DOI: 10.1002/pro.70027

実験手法

ELECTRON MICROSCOPY (2.27 Å)