2BF4 | pdb_00002bf4

A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductases.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.261 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2BF4

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

A Second Fmn-Binding Site in Yeast Nadph-Cytochrome P450 Reductase Suggests a Mechanism of Electron Transfer by Diflavin Reductases.

Lamb, D.C.Kim, Y.Yermalitskaya, L.V.Yermalitsky, V.N.Lepesheva, G.I.Kelly, S.L.Waterman, M.R.Podust, L.M.

(2006) Structure 14: 51

  • DOI: https://doi.org/10.1016/j.str.2005.09.015
  • Primary Citation Related Structures: 
    2BF4, 2BN4

  • PubMed Abstract: 

    NADPH-cytochrome P450 reductase transfers two reducing equivalents derived from a hydride ion of NADPH via FAD and FMN to the large family of microsomal cytochrome P450 monooxygenases in one-electron transfer steps. The mechanism of electron transfer by diflavin reductases remains elusive and controversial. Here, we determined the crystal structure of truncated yeast NADPH-cytochrome P450 reductase, which is functionally active toward its physiological substrate cytochrome P450, and discovered a second FMN binding site at the interface of the connecting and FMN binding domains. The two FMN binding sites have different accessibilities to the bulk solvent and different amino acid environments, suggesting stabilization of different electronic structures of the reduced flavin. Since only one FMN cofactor is required for function, a hypothetical mechanism of electron transfer is discussed that proposes shuttling of a single FMN between these two sites coupled with the transition between two semiquinone forms, neutral (blue) and anionic (red).


  • Organizational Affiliation
    • Wolfson Laboratory of P450 Biodiversity, Swansea Medical School University of Wales Swansea, Swansea, Wales SA2 8PP, UK.

Macromolecule Content 

  • Total Structure Weight: 156.86 kDa 
  • Atom Count: 10,624 
  • Modeled Residue Count: 1,290 
  • Deposited Residue Count: 1,364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADPH-CYTOCHROME P450 REDUCTASE
A, B
682Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.6.2.4
UniProt
Find proteins for P16603 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16603 
Go to UniProtKB:  P16603
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16603
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP

Query on NAP



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
K [auth B],
L [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SO4

Query on SO4



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.261 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.751α = 90
b = 87.094β = 90
c = 259.59γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other