3KP9

Structure of a bacterial homolog of vitamin K epoxide reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a bacterial homologue of vitamin K epoxide reductase.

Li, W.Schulman, S.Dutton, R.J.Boyd, D.Beckwith, J.Rapoport, T.A.

(2010) Nature 463: 507-512

  • DOI: 10.1038/nature08720
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vitamin K epoxide reductase (VKOR) generates vitamin K hydroquinone to sustain gamma-carboxylation of many blood coagulation factors. Here, we report the 3.6 A crystal structure of a bacterial homologue of VKOR from Synechococcus sp. The structure sh ...

    Vitamin K epoxide reductase (VKOR) generates vitamin K hydroquinone to sustain gamma-carboxylation of many blood coagulation factors. Here, we report the 3.6 A crystal structure of a bacterial homologue of VKOR from Synechococcus sp. The structure shows VKOR in complex with its naturally fused redox partner, a thioredoxin-like domain, and corresponds to an arrested state of electron transfer. The catalytic core of VKOR is a four transmembrane helix bundle that surrounds a quinone, connected through an additional transmembrane segment with the periplasmic thioredoxin-like domain. We propose a pathway for how VKOR uses electrons from cysteines of newly synthesized proteins to reduce a quinone, a mechanism confirmed by in vitro reconstitution of vitamin K-dependent disulphide bridge formation. Our results have implications for the mechanism of the mammalian VKOR and explain how mutations can cause resistance to the VKOR inhibitor warfarin, the most commonly used oral anticoagulant.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA. weikai@crystal.harvard.edu




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
mpstruc
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 2 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
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.251 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 136.942α = 90.00
b = 136.942β = 90.00
c = 68.480γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance