spacer
spacer

PDBsum entry 1o9j

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1o9j
Jmol
Contents
Protein chains
494 a.a. *
Ligands
NAD ×4
DTT
DTU
Waters ×454
* Residue conservation analysis
PDB id:
1o9j
Name: Oxidoreductase
Title: The x-ray crystal structure of eta-crystallin
Structure: Aldehyde dehydrogenase, cytosolic 1. Chain: a, b, c, d. Synonym: eta-crystallin, aldh class 1. Engineered: yes. Other_details: NAD cofactor present
Source: Elephantulus edwardii. Cape long-eared elephant shrew. Organism_taxid: 28737. Organ: eye. Tissue: lens. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.4Å     R-factor:   0.184     R-free:   0.254
Authors: A.G.Purkiss,R.Van Montfort,G.Wistow,C.Slingsby
Key ref:
O.A.Bateman et al. (2003). Crystal structure of eta-crystallin: adaptation of a class 1 aldehyde dehydrogenase for a new role in the eye lens. Biochemistry, 42, 4349-4356. PubMed id: 12693930 DOI: 10.1021/bi027367w
Date:
15-Dec-02     Release date:   17-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q28399  (ALDH1_ELEED) -  Aldehyde dehydrogenase, cytosolic 1
Seq:
Struc:
501 a.a.
494 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.2.1.3  - Aldehyde dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + NAD+ + H2O = a carboxylate + NADH
aldehyde
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
+ H(2)O
= carboxylate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi027367w Biochemistry 42:4349-4356 (2003)
PubMed id: 12693930  
 
 
Crystal structure of eta-crystallin: adaptation of a class 1 aldehyde dehydrogenase for a new role in the eye lens.
O.A.Bateman, A.G.Purkiss, R.van Montfort, C.Slingsby, C.Graham, G.Wistow.
 
  ABSTRACT  
 
Eta-crystallin is a retinal dehydrogenase that has acquired a role as a structural protein in the eye lens of elephant shrews, members of an ancient order of mammals. While it retains some activity toward retinal, which is oxidized to retinoic acid, the protein has acquired a number of specific sequence changes that have presumably been selected to enhance the lens role. The crystal structure of eta-crystallin, in common with class 1 and 2 ALDHs, is a dimer of dimers. It has a better-defined NAD binding site than those of related mammalian ALDH1 enzymes with the cofactor bound in the "hydride transfer" position in all four monomers with small differences about the dimer dyads. Although the active site is well conserved, the substrate-binding site is larger in eta-crystallin, and there are some mutations to the substrate access tunnel that might affect binding or release of substrate and product. It is possible that eta-crystallin has lost flexibility to improve its role in the lens. Enhanced binding of cofactor could enable it to act as a UV/blue light filter in the lens, improving visual acuity. The structure not only gives a view of a "natural mutant" of ALDH1 illustrating the adaptive conflict that can arise in multifunctional proteins, but also provides a well-ordered NAD binding site structure for this class of enzymes with important roles in development and health.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18974821 M.Punta, and Y.Ofran (2008).
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function.
  PLoS Comput Biol, 4, e1000160.  
16835232 S.Watanabe, T.Kodaki, and K.Makino (2006).
A novel alpha-ketoglutaric semialdehyde dehydrogenase: evolutionary insight into an alternative pathway of bacterial L-arabinose metabolism.
  J Biol Chem, 281, 28876-28888.  
15877277 G.Sriram, J.A.Martinez, E.R.McCabe, J.C.Liao, and K.M.Dipple (2005).
Single-gene disorders: what role could moonlighting enzymes play?
  Am J Hum Genet, 76, 911-924.  
15299009 T.Bordelon, S.K.Montegudo, S.Pakhomova, M.L.Oldham, and M.E.Newcomer (2004).
A disorder to order transition accompanies catalysis in retinaldehyde dehydrogenase type II.
  J Biol Chem, 279, 43085-43091.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.