4NV2

C50A mutant of Synechococcus VKOR, C2221 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer.

Liu, S.Cheng, W.Fowle Grider, R.Shen, G.Li, W.

(2014) Nat Commun 5: 3110-3110

  • DOI: 10.1038/ncomms4110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The intramembrane vitamin K epoxide reductase (VKOR) supports blood coagulation in humans and is the target of the anticoagulant warfarin. VKOR and its homologues generate disulphide bonds in organisms ranging from bacteria to humans. Here, to better ...

    The intramembrane vitamin K epoxide reductase (VKOR) supports blood coagulation in humans and is the target of the anticoagulant warfarin. VKOR and its homologues generate disulphide bonds in organisms ranging from bacteria to humans. Here, to better understand the mechanism of VKOR catalysis, we report two crystal structures of a bacterial VKOR captured in different reaction states. These structures reveal a short helix at the hydrophobic active site of VKOR that alters between wound and unwound conformations. Motions of this 'horizontal helix' promote electron transfer by regulating the positions of two cysteines in an adjacent loop. Winding of the helix separates these 'loop cysteines' to prevent backward electron flow. Despite these motions, hydrophobicity at the active site is maintained to facilitate VKOR catalysis. Biochemical experiments suggest that several warfarin-resistant mutations act by changing the conformation of the horizontal helix. Taken together, these studies provide a comprehensive understanding of VKOR function.


    Organizational Affiliation

    1] Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VKORC1/thioredoxin domain protein
A
291Synechococcus sp. (strain JA-2-3B'a(2-13))Mutation(s): 1 
EC: 1.17.4.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Vitamin K epoxide reductase
Find proteins for Q2JJF6 (Synechococcus sp. (strain JA-2-3B'a(2-13)))
Go to UniProtKB:  Q2JJF6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

Download SDF File 
Download CCD File 
A
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 130.800α = 90.00
b = 142.490β = 90.00
c = 69.010γ = 90.00
Software Package:
Software NamePurpose
PARROTphasing
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release