8QUO

Cryo-EM structure of coproheme decarboxylase from Corynebacterium diphtheriae in complex with heme b

Summary for 8QUO

• Entry DOI: 10.2210/pdb8quo/pdb
• EMDB information: 18662
• Descriptor: Coproheme decarboxylase, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: heme binding protein, heme biosynthesis, actinobacteria, oxidoreductase
• Biological source: Corynebacterium diphtheriae
• Total number of polymer chains: 5
• Total formula weight: 139527.24

Authors

Patil, G.,Guo, Y.,Borek, D.,Hofbauer, S. (deposition date: 2023-10-16, release date: 2025-02-05)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (1.94 Å)