4F2Z

Crystal structure of RPE65 in a lipid environment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis.

Kiser, P.D.Farquhar, E.R.Shi, W.Sui, X.Chance, M.R.Palczewski, K.

(2012) Proc.Natl.Acad.Sci.USA 109: E2747-E2756

  • DOI: 10.1073/pnas.1212025109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RPE65 is a key metalloenzyme responsible for maintaining visual function in vertebrates. Despite extensive research on this membrane-bound retinoid isomerase, fundamental questions regarding its enzymology remain unanswered. Here, we report the cryst ...

    RPE65 is a key metalloenzyme responsible for maintaining visual function in vertebrates. Despite extensive research on this membrane-bound retinoid isomerase, fundamental questions regarding its enzymology remain unanswered. Here, we report the crystal structure of RPE65 in a membrane-like environment. These crystals, obtained from enzymatically active, nondelipidated protein, displayed an unusual packing arrangement wherein RPE65 is embedded in a lipid-detergent sheet. Structural differences between delipidated and nondelipidated RPE65 uncovered key residues involved in substrate uptake and processing. Complementary iron K-edge X-ray absorption spectroscopy data established that RPE65 as isolated contained a divalent iron center and demonstrated the presence of a tightly bound ligand consistent with a coordinated carboxylate group. These results support the hypothesis that the Lewis acidity of iron could be used to promote ester dissociation and generation of a carbocation intermediate required for retinoid isomerization.


    Organizational Affiliation

    Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA. pdk7@case.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoid isomerohydrolase
A, E
533Bos taurusMutation(s): 0 
Gene Names: RPE65
EC: 3.1.1.64
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Isomerases
Protein: 
RPE65 visual cycle retinoid isomerase
Find proteins for Q28175 (Bos taurus)
Go to Gene View: RPE65
Go to UniProtKB:  Q28175
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, E
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.799α = 90.00
b = 100.234β = 90.00
c = 277.588γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references