6J79 | pdb_00006j79

Fusion protein of heme oxygenase-1 and NADPH-cytochrome P450 reductase (13aa)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 
    0.248 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6J79

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a NADPH-cytochrome P450 oxidoreductase (CYPOR) and heme oxygenase 1 fusion protein implies a conformational change in CYPOR upon NADPH/NADP+binding.

Sugishima, M.Sato, H.Wada, K.Yamamoto, K.

(2019) FEBS Lett 593: 868-875

  • DOI: https://doi.org/10.1002/1873-3468.13360
  • Primary Citation Related Structures: 
    6J79, 6J7A, 6J7I

  • PubMed Abstract: 

    Heme oxygenase-1 (HMOX1) catalyzes heme degradation utilizing reducing equivalents supplied from NADPH-cytochrome P450 reductase (CYPOR). Recently, we determined the complex structure of NADP + -bound open-conformation stabilized CYPOR and heme-HMOX1, but the resolution was limited to 4.3 Å. Here, we determined the crystal structure of the fusion protein of open-conformation stabilized CYPOR and heme-HMOX1 at 3.25 Å resolution. Unexpectedly, no NADP + was bound to this fusion protein in the crystal. Structural comparison of the NADP + -bound complex and the NADP + -free fusion protein suggests that NADP + binding regulates the conformational change in the FAD-binding domain of CYPOR. As a result of this change, the FMN-binding domain of CYPOR approaches heme-bound HMOX1 upon NADP + binding to enhance the electron-transfer efficiency from FMN to heme.


  • Organizational Affiliation
    • Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan.

Macromolecule Content 

  • Total Structure Weight: 202.4 kDa 
  • Atom Count: 13,345 
  • Modeled Residue Count: 1,629 
  • Deposited Residue Count: 1,742 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heme oxygenase 1,NADPH--cytochrome P450 reductase
A, B
871Rattus norvegicusMutation(s): 2 
Gene Names: Hmox1Por
EC: 1.14.14.18 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P00388 (Rattus norvegicus)
Explore P00388 
Go to UniProtKB:  P00388
Find proteins for P06762 (Rattus norvegicus)
Explore P06762 
Go to UniProtKB:  P06762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP06762P00388
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free:  0.248 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.36α = 90
b = 159.78β = 90
c = 189.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16K07280
Japan Society for the Promotion of ScienceJapan25840026

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description