1BI9

RETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 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

  • 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 productio ...

    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: 
    • 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
    • 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.,Sect.D 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

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RETINAL DEHYDROGENASE TYPE II
A, B, C, D
499Rattus norvegicusMutation(s): 0 
Gene Names: Aldh1a2 (Raldh2)
EC: 1.2.1.36
Find proteins for Q63639 (Rattus norvegicus)
Go to UniProtKB:  Q63639
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAD
Query on NAD
Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 149.800α = 90.00
b = 167.300β = 90.00
c = 107.500γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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