1BI9

RETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of retinal dehydrogenase type II at 2.7 A resolution: implications for retinal specificity.

Lamb, A.L.Newcomer, M.E.

(1999) Biochemistry 38: 6003-6011

  • DOI: 10.1021/bi9900471
  • Primary Citation of Related Structures:  
    1BI9

  • PubMed Abstract: 
  • Retinoic acid, a hormonally active form of vitamin A, is produced in vivo in a two step process: retinol is oxidized to retinal and retinal is oxidized to retinoic acid. Retinal dehydrogenase type II (RalDH2) catalyzes this last step in the production of retinoic acid in the early embryo, possibly producing this putative morphogen to initiate pattern formation ...

    Retinoic acid, a hormonally active form of vitamin A, is produced in vivo in a two step process: retinol is oxidized to retinal and retinal is oxidized to retinoic acid. Retinal dehydrogenase type II (RalDH2) catalyzes this last step in the production of retinoic acid in the early embryo, possibly producing this putative morphogen to initiate pattern formation. The enzyme is also found in the adult animal, where it is expressed in the testis, lung, and brain among other tissues. The crystal structure of retinal dehydrogenase type II cocrystallized with nicotinamide adenine dinucleotide (NAD) has been determined at 2.7 A resolution. The structure was solved by molecular replacement using the crystal structure of a mitochondrial aldehyde dehydrogenase (ALDH2) as a model. Unlike what has been described for the structures of two aldehyde dehydrogenases involved in the metabolism of acetaldehyde, the substrate access channel is not a preformed cavity into which acetaldehyde can readily diffuse. Retinal dehydrogenase appears to utilize a disordered loop in the substrate access channel to discriminate between retinaldehyde and short-chain aldehydes.


    Related Citations: 
    • Purification, Crystallization and Preliminary X-Ray Diffraction Studies of Retinal Dehydrogenase Type II
      Lamb, A.L., Wang, X., Napoli, J.L., Newcomer, M.E.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 639
    • Restricted Expression and Retinoic Acid-Induced Downregulation of the Retinaldehyde Dehydrogenase Type 2 (Raldh-2) Gene During Mouse Development
      Niederreither, K., Mccaffery, P., Drager, U.C., Chambon, P., Dolle, P.
      (1997) Mech Dev 62: 67
    • Cloning of a Cdna Encoding an Aldehyde Dehydrogenase and its Expression in Escherichia Coli. Recognition of Retinal as Substrate
      Wang, X., Penzes, P., Napoli, J.L.
      (1996) J Biol Chem 271: 16288

    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINAL DEHYDROGENASE TYPE IIA, B, C, D499Rattus norvegicusMutation(s): 0 
Gene Names: Aldh1a2Raldh2
EC: 1.2.1 (PDB Primary Data), 1.2.1.36 (UniProt)
UniProt
Find proteins for Q63639 (Rattus norvegicus)
Explore Q63639 
Go to UniProtKB:  Q63639
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], I [auth C], J [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth C], H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.8α = 90
b = 167.3β = 90
c = 107.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance