Crystal Structure Of An Artificial Metalloprotein: Fe(10-CH2CH2COOH-Salophen)/Wild Type Heme oxygenase

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Design of metal cofactors activated by a protein-protein electron transfer system.

Ueno, T.Yokoi, N.Unno, M.Matsui, T.Tokita, Y.Yamada, M.Ikeda-Saito, M.Nakajima, H.Watanabe, Y.

(2006) Proc Natl Acad Sci U S A 103: 9416-9421

  • DOI: https://doi.org/10.1073/pnas.0510968103
  • Primary Citation of Related Structures:  
    1WZD, 1WZF, 1WZG

  • PubMed Abstract: 

    Protein-to-protein electron transfer (ET) is a critical process in biological chemistry for which fundamental understanding is expected to provide a wealth of applications in biotechnology. Investigations of protein-protein ET systems in reductive activation of artificial cofactors introduced into proteins remains particularly challenging because of the complexity of interactions between the cofactor and the system contributing to ET. In this work, we construct an artificial protein-protein ET system, using heme oxygenase (HO), which is known to catalyze the conversion of heme to biliverdin. HO uses electrons provided from NADPH/cytochrome P450 reductase (CPR) through protein-protein complex formation during the enzymatic reaction. We report that a Fe(III)(Schiff-base), in the place of the active-site heme prosthetic group of HO, can be reduced by NADPH/CPR. The crystal structure of the Fe(10-CH(2)CH(2)COOH-Schiff-base).HO composite indicates the presence of a hydrogen bond between the propionic acid carboxyl group and Arg-177 of HO. Furthermore, the ET rate from NADPH/CPR to the composite is 3.5-fold faster than that of Fe(Schiff-base).HO, although the redox potential of Fe(10-CH(2)CH(2)COOH-Schiff-base).HO (-79 mV vs. NHE) is lower than that of Fe(Schiff-base).HO (+15 mV vs. NHE), where NHE is normal hydrogen electrode. This work describes a synthetic metal complex activated by means of a protein-protein ET system, which has not previously been reported. Moreover, the result suggests the importance of the hydrogen bond for the ET reaction of HO. Our Fe(Schiff-base).HO composite model system may provide insights with regard to design of ET biosystems for sensors, catalysts, and electronics devices.

  • Organizational Affiliation

    Research Center for Materials Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heme oxygenase
A, B
215Corynebacterium diphtheriaeMutation(s): 0 
Find proteins for Q54AI1 (Corynebacterium diphtheriae)
Explore Q54AI1 
Go to UniProtKB:  Q54AI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54AI1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on YOK

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
C23 H18 Fe N2 O4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.257α = 90
b = 63.009β = 98.52
c = 78.159γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations