3WKT

Complex structure of an open form of NADPH-cytochrome P450 reductase and heme oxygenase-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the electron transfer from an open form of NADPH-cytochrome P450 oxidoreductase to heme oxygenase.

Sugishima, M.Sato, H.Higashimoto, Y.Harada, J.Wada, K.Fukuyama, K.Noguchi, M.

(2014) Proc.Natl.Acad.Sci.USA 111: 2524-2529

  • DOI: 10.1073/pnas.1322034111

  • PubMed Abstract: 
  • NADPH-cytochrome P450 oxidoreductase (CPR) supplies electrons to various heme proteins including heme oxygenase (HO), which is a key enzyme for heme degradation. Electrons from NADPH flow first to flavin adenine dinucleotide, then to flavin mononucle ...

    NADPH-cytochrome P450 oxidoreductase (CPR) supplies electrons to various heme proteins including heme oxygenase (HO), which is a key enzyme for heme degradation. Electrons from NADPH flow first to flavin adenine dinucleotide, then to flavin mononucleotide (FMN), and finally to heme in the redox partner. For electron transfer from CPR to its redox partner, the ''closed-open transition'' of CPR is indispensable. Here, we demonstrate that a hinge-shortened CPR variant, which favors an open conformation, makes a stable complex with heme-HO-1 and can support the HO reaction, although its efficiency is extremely limited. Furthermore, we determined the crystal structure of the CPR variant in complex with heme-HO-1 at 4.3-Å resolution. The crystal structure of a complex of CPR and its redox partner was previously unidentified. The distance between heme and FMN in this complex (6 Å) implies direct electron transfer from FMN to heme.


    Organizational Affiliation

    Department of Medical Biochemistry and Department of Chemistry, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH-cytochrome P450 reductase
A, B
618Rattus norvegicusGene Names: Por
EC: 1.6.2.4
Find proteins for P00388 (Rattus norvegicus)
Go to UniProtKB:  P00388
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heme oxygenase 1
C, D
267Rattus norvegicusGene Names: Hmox1
EC: 1.14.14.18
Find proteins for P06762 (Rattus norvegicus)
Go to UniProtKB:  P06762
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 290.336α = 90.00
b = 290.336β = 90.00
c = 83.646γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
BSSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references