4NV5

C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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:  
    4NV5, 4NV6, 4NV2

  • 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 understand the mechanism of VKOR catalysis, we report two crystal structures of a bacterial VKOR captured in different reaction states ...

    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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VKORC1/thioredoxin domain proteinA, B291Synechococcus sp. JA-2-3B'a(2-13)Mutation(s): 1 
Gene Names: CYB_2278
EC: 1.17.4
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Vitamin K epoxide reductase, C50A mutant in dehydrated state
Find proteins for Q2JJF6 (Synechococcus sp. (strain JA-2-3B'a(2-13)))
Explore Q2JJF6 
Go to UniProtKB:  Q2JJF6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.842α = 90
b = 118.822β = 89.85
c = 68.034γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PARROTphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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