4CIZ | pdb_00004ciz

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

PDB DOI: https://doi.org/10.2210/pdb4CIZ/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-12-18 Released: 2014-01-08
Deposition Author(s): 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.265 (Depositor), 0.285 (DCC)
R-Value Work:
0.234 (Depositor), 0.245 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 24328211 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja411366w
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 36.95 kDa
Atom Count: 2,345
Modeled Residue Count: 284
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINALDEHYDE-BINDING PROTEIN 1	A	317	Homo sapiens	Mutation(s): 0
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12271
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.265 (Depositor), 0.285 (DCC)
R-Value Work: 0.234 (Depositor), 0.245 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.556	α = 90
b = 70.556	β = 90
c = 299.747	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-08

Deposition Author(s):

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