4F3D | pdb_00004f3d

Structure of RPE65: P65 crystal form grown in Fos-Choline-10

• PDB DOI: https://doi.org/10.2210/pdb4F3D/pdb

• Classification: ISOMERASE, HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2012-05-09 Released: 2012-10-03 
• Deposition Author(s): Kiser, P.D., Palczewski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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 U S A 109: E2747-E2756

• PubMed: 23012475 
• DOI: https://doi.org/10.1073/pnas.1212025109
• Primary Citation Related Structures: 
  4F2Z, 4F30, 4F3A, 4F3D


• 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 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.

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Organizational Affiliation: 
• Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 122.46 kDa 
• Atom Count: 8,421 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoid isomerohydrolase	A, B	533	Bos taurus	Mutation(s): 0  EC: 3.1.1.64 (PDB Primary Data), 5.3.3.22 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q28175 (Bos taurus) Explore Q28175  Go to UniProtKB:  Q28175

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETX	D [auth A], E [auth A], G [auth B]	2-ETHOXYETHANOL C4 H10 O2 ZNQVEEAIQZEUHB-UHFFFAOYSA-N
FE2	C [auth A], F [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.258	α = 90
b = 175.258	β = 90
c = 86.449	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Kiser, P.D., Palczewski, K.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description