5T2K image
Deposition Date 2016-08-23
Release Date 2017-01-18
Last Version Date 2023-10-04
Entry Detail
PDB ID:
5T2K
Keywords:
Title:
Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.17
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Putative heme-dependent peroxidase GT50_08830
Gene (Uniprot):chdC
Chain IDs:A, B, C, D, E
Chain Length:248
Number of Molecules:5
Biological Source:Geobacillus stearothermophilus 10
Ligand Molecules
Primary Citation
Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ).
J. Am. Chem. Soc. 139 1900 1911 (2017)
PMID: 27936663 DOI: 10.1021/jacs.6b11324

Abstact

Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.

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Primary Citation of related structures