9QDT image
Deposition Date 2025-03-06
Release Date 2025-07-30
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9QDT
Keywords:
Title:
Cytochrome c peroxidase YhjA
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.57 Å
R-Value Free:
0.22
R-Value Work:
0.17
Space Group:
P 41 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable cytochrome c peroxidase
Gene (Uniprot):ccp
Chain IDs:A
Chain Length:417
Number of Molecules:1
Biological Source:Escherichia coli K-12
Primary Citation
Escherichia coli Triheme Enzyme YhjA: Structure and Reactivity.
Biochemistry 64 3322 3332 (2025)
PMID: 40669070 DOI: 10.1021/acs.biochem.5c00202

Abstact

It has been recently realized that some Gram-negative organisms such as Escherichia coli produce a multiheme cytochrome c to serve as a quinol peroxidase that couples electrons from the quinol pool directly to H2O2. The E. coli version of this enzyme, termed YhjA, has been predicted to be a member of the bacterial cytochrome c peroxidase (bCCP) superfamily, where a novel N-terminal single-heme binding domain is fused to the canonical bCCP diheme domain found widely in Gram-negative bacteria. Here, we present an X-ray crystal structure of YhjA, revealing the triheme architecture that nature has employed to couple the quinol pool to the reduction of H2O2. We also show kinetic, spectroscopic, and electrochemical data that detail the differences between the three hemes that are observed in the structure, where two of the heme irons are both six-coordinate, ligated by Met and His residues, and the third peroxidatic heme is found to be five-coordinate. Electrocatalytic voltammetry of YhjA illustrates how the high-potential hemes serve as relays to the peroxidatic active site. Together, these data suggest a model of the catalytic chemistry of YhjA, illustrating how this member of the bCCP family may react with substrates and engage in multielectron redox reactions.

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