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PDBsum entry 3es9

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3es9
Jmol
Contents
Protein chains
603 a.a. *
515 a.a. *
435 a.a. *
Ligands
FMN
FAD ×3
NAP ×2
* Residue conservation analysis
PDB id:
3es9
Name: Oxidoreductase
Title: NADPH-cytochrome p450 reductase in an open conformation
Structure: NADPH--cytochrome p450 reductase. Chain: a, b, c. Synonym: cpr, p450r. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: cypor, por. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.40Å     R-factor:   0.219     R-free:   0.279
Authors: D.Hamdane,C.Xia,S.-C.Im,H.Zhang,J.-J.Kim,L.Waskell
Key ref:
D.Hamdane et al. (2009). Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450. J Biol Chem, 284, 11374-11384. PubMed id: 19171935 DOI: 10.1074/jbc.M807868200
Date:
05-Oct-08     Release date:   20-Jan-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00388  (NCPR_RAT) -  NADPH--cytochrome P450 reductase
Seq:
Struc:
 
Seq:
Struc:
678 a.a.
603 a.a.
Protein chain
Pfam   ArchSchema ?
P00388  (NCPR_RAT) -  NADPH--cytochrome P450 reductase
Seq:
Struc:
 
Seq:
Struc:
678 a.a.
515 a.a.
Protein chain
Pfam   ArchSchema ?
P00388  (NCPR_RAT) -  NADPH--cytochrome P450 reductase
Seq:
Struc:
 
Seq:
Struc:
678 a.a.
435 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.1.6.2.4  - NADPH--hemoprotein reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + n oxidized hemoprotein = NADP+ + n reduced hemoprotein
NADPH
Bound ligand (Het Group name = NAP)
corresponds exactly
+ n oxidized hemoprotein
= NADP(+)
+ n reduced hemoprotein
      Cofactor: FAD; FMN
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
FMN
Bound ligand (Het Group name = FMN) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   6 terms 
  Biological process     regulation of growth plate cartilage chondrocyte proliferation   24 terms 
  Biochemical function     electron carrier activity     13 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M807868200 J Biol Chem 284:11374-11384 (2009)
PubMed id: 19171935  
 
 
Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450.
D.Hamdane, C.Xia, S.C.Im, H.Zhang, J.J.Kim, L.Waskell.
 
  ABSTRACT  
 
NADPH-cytochrome P450 oxidoreductase (CYPOR) catalyzes the transfer of electrons to all known microsomal cytochromes P450. A CYPOR variant, with a 4-amino acid deletion in the hinge connecting the FMN domain to the rest of the protein, has been crystallized in three remarkably extended conformations. The variant donates an electron to cytochrome P450 at the same rate as the wild-type, when provided with sufficient electrons. Nevertheless, it is defective in its ability to transfer electrons intramolecularly from FAD to FMN. The three extended CYPOR structures demonstrate that, by pivoting on the C terminus of the hinge, the FMN domain of the enzyme undergoes a structural rearrangement that separates it from FAD and exposes the FMN, allowing it to interact with its redox partners. A similar movement most likely occurs in the wild-type enzyme in the course of transferring electrons from FAD to its physiological partner, cytochrome P450. A model of the complex between an open conformation of CYPOR and cytochrome P450 is presented that satisfies mutagenesis constraints. Neither lengthening the linker nor mutating its sequence influenced the activity of CYPOR. It is likely that the analogous linker in other members of the diflavin family functions in a similar manner.
 
  Selected figure(s)  
 
Figure 1.
Crystal structure of three conformations of ΔTGEE. Three conformations of ΔTGEE and the wild-type structure are compared. The relative orientations of FMN domains of Mol A (magenta; FMN is green), Mol B (blue; FMN is red), and Mol C (gray; FMN is yellow) of ΔTGEE, when their FAD domains are superimposed onto the wild-type CYPOR structure (gold; FMN is blue, and FAD is black). For clarity, only the FAD domain of wild-type is shown. The hinges are depicted as thick tubes in their respective colors, and the flavins are shown as stick models. The FMN domain moves away from the FAD domain by extending the hinge and simultaneously rotating about a pivot point, which is located on the backbone carbonyl of the C-terminal residue of the hinge (Arg-243 in wild-type numbering). Note that the FMN isoalloxazine ring is exposed to solvent in all three conformations such that its dimethyl group can interact with cyt P450.
Figure 7.
Model of a complex between cyt P450 2B4 and Mol A of ΔTGEE. A, surface representation of the model complex: pink, cyt P450; yellow, FMN domain; and green, FAD domain. B and C, electrostatic surface of the interfaces of cyt P450 (B) and CYPOR (C) where blue represents a positively charged surface and red is a negative surface. The heme and flavin are shown below the surface of cyt P450 and CYPOR, respectively. D, stick representation of heme (red) and FMN (yellow) cofactors in the complex showing their relative orientations and the two residues (Phe-429 and Glu-549) of cyt P450 that lie in between the two redox cofactors. E and F, interfaces of docked CYPOR and cyt P450. Five pairs of salt bridges are shown at the interface between cyt P450 and CYPOR. The salt-bridge pairs are marked with the same letters, i.e. R122(a) of cyt P450 pairs with E92(a) of CYPOR. Arg-443 of cyt P450 forms an H-bond with Tyr-178 of the CYPOR. The views are the same as those in panels B and C, respectively.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 11374-11384) copyright 2009.  
  Figures were selected by the author.  
 
 
    Author's comment    
 
  NADPH-cytochrome P450 oxidoreductase (CYPOR)is a multidomain flavoprotein that reduces P450 enzymes. All previously determined crystal structures of CYPOR are in a closed conformation in which the FMN domain is not capable of interacting with its redox partners. This work presents, for the first time, three open conformations of CYPOR capable of reducing P450. This was achieved using a variant form of CYPOR containing a four-amino acid deletion (ΔTGEE) in the hinge region connecting the FMN domain to the rest of the protein.
Jung-Ja Kim
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265736 L.Aigrain, D.Pompon, and G.Truan (2011).
Role of the interface between the FMN and FAD domains in the control of redox potential and electronic transfer of NADPH-cytochrome P450 reductase.
  Biochem J, 435, 197-206.  
  21472912 S.E.Rigby, X.Lou, H.S.Toogood, K.R.Wolthers, and N.S.Scrutton (2011).
ELDOR spectroscopy reveals that energy landscapes in human methionine synthase reductase are extensively remodelled following ligand and partner protein binding.
  Chembiochem, 12, 863-867.  
20718865 A.Welland, and S.Daff (2010).
Conformation-dependent hydride transfer in neuronal nitric oxide synthase reductase domain.
  FEBS J, 277, 3833-3843.  
19884324 C.C.Marohnic, S.P.Panda, K.McCammon, J.Rueff, B.S.Masters, and M.Kranendonk (2010).
Human cytochrome P450 oxidoreductase deficiency caused by the Y181D mutation: molecular consequences and rescue of defect.
  Drug Metab Dispos, 38, 332-340.  
20026040 D.R.Davydov, E.V.Sineva, S.Sistla, N.Y.Davydova, D.J.Frank, S.G.Sligar, and J.R.Halpert (2010).
Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.
  Biochim Biophys Acta, 1797, 378-390.  
20879989 Y.Farooq, and G.C.Roberts (2010).
Kinetics of electron transfer between NADPH-cytochrome P450 reductase and cytochrome P450 3A4.
  Biochem J, 432, 485-493.  
19908820 A.Das, and S.G.Sligar (2009).
Modulation of the cytochrome P450 reductase redox potential by the phospholipid bilayer.
  Biochemistry, 48, 12104-12112.  
19690675 C.Feng, and G.Tollin (2009).
Regulation of interdomain electron transfer in the NOS output state for NO production.
  Dalton Trans, (), 6692-6700.  
19737939 C.Xia, I.Misra, T.Iyanagi, and J.J.Kim (2009).
Regulation of interdomain interactions by calmodulin in inducible nitric-oxide synthase.
  J Biol Chem, 284, 30708-30717.  
19583767 D.J.Stuehr, J.Tejero, and M.M.Haque (2009).
Structural and mechanistic aspects of flavoproteins: electron transfer through the nitric oxide synthase flavoprotein domain.
  FEBS J, 276, 3959-3974.  
19858215 J.Ellis, A.Gutierrez, I.L.Barsukov, W.C.Huang, J.G.Grossmann, and G.C.Roberts (2009).
Domain motion in cytochrome P450 reductase: conformational equilibria revealed by NMR and small-angle x-ray scattering.
  J Biol Chem, 284, 36628-36637.  
19956630 Y.Hong, H.Li, J.Ye, Y.Miki, Y.C.Yuan, H.Sasano, D.B.Evans, and S.Chen (2009).
Epitope characterization of an aromatase monoclonal antibody suitable for the assessment of intratumoral aromatase activity.
  PLoS One, 4, e8050.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.