4CJ6

Crystal structure of the complex of the Cellular Retinal Binding Protein Mutant R234W with 9-cis-retinal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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This is version 1.2 of the entry. See complete history


Literature

Human Cellular Retinaldehyde-Binding Protein Has Secondary Thermal 9-Cis-Retinal Isomerase Activity.

Bolze, C.S.Helbling, R.E.Owen, R.L.Pearson, A.R.Pompidor, G.Dworkowski, F.Fuchs, M.R.Furrer, J.Golczak, M.Palczewski, K.Cascella, M.Stocker, A.

(2014) J Am Chem Soc 136: 137

  • DOI: https://doi.org/10.1021/ja411366w
  • Primary Citation of Related Structures:  
    4CIZ, 4CJ6

  • PubMed Abstract: 

    Cellular retinaldehyde-binding protein (CRALBP) chaperones 11-cis-retinal to convert opsin receptor molecules into photosensitive retinoid pigments of the eye. We report a thermal secondary isomerase activity of CRALBP when bound to 9-cis-retinal. UV/vis and (1)H NMR spectroscopy were used to characterize the product as 9,13-dicis-retinal. The X-ray structure of the CRALBP mutant R234W:9-cis-retinal complex at 1.9 Å resolution revealed a niche in the binding pocket for 9-cis-aldehyde different from that reported for 11-cis-retinal. Combined computational, kinetic, and structural data lead us to propose an isomerization mechanism catalyzed by a network of buried waters. Our findings highlight a specific role of water molecules in both CRALBP-assisted specificity toward 9-cis-retinal and its thermal isomerase activity yielding 9,13-dicis-retinal. Kinetic data from two point mutants of CRALBP support an essential role of Glu202 as the initial proton donor in this isomerization reaction.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, and ‡Graduate School for Cellular and Biomedical Sciences, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RETINALDEHYDE-BINDING PROTEIN 1317Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P12271 (Homo sapiens)
Explore P12271 
Go to UniProtKB:  P12271
PHAROS:  P12271
GTEx:  ENSG00000140522 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12271
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.87α = 90
b = 57.918β = 122.88
c = 75.206γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description