9QDT | pdb_00009qdt

Cytochrome c peroxidase YhjA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.222 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Escherichia coli Triheme Enzyme YhjA: Structure and Reactivity.

Hewitt, P.Seidel, J.Wust, A.Smith, M.Maiocco, S.J.Shternberg, S.Hoffmann, M.Spatzal, T.Gerhardt, S.Einsle, O.Elliott, S.J.

(2025) Biochemistry 64: 3322-3332

  • DOI: https://doi.org/10.1021/acs.biochem.5c00202
  • Primary Citation Related Structures: 
    9QDT

  • PubMed Abstract: 

    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 H 2 O 2 . 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 H 2 O 2 . 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.


  • Organizational Affiliation
    • Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States.

Macromolecule Content 

  • Total Structure Weight: 48.72 kDa 
  • Atom Count: 3,467 
  • Modeled Residue Count: 417 
  • Deposited Residue Count: 417 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable cytochrome c peroxidase417Escherichia coli K-12Mutation(s): 0 
Gene Names: yhjAb3518JW3486
EC: 1.11.1.5 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for P37197 (Escherichia coli (strain K12))
Explore P37197 
Go to UniProtKB:  P37197
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37197
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
(Subject of Investigation/LOI)

Query on HEC



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
D [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
EPE

Query on EPE



Download:Ideal Coordinates CCD File
H [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.222 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.204 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.42α = 90
b = 101.42β = 90
c = 134.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany403222702

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references