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PDBsum entry 3gfb

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3gfb
Jmol
Contents
Protein chains
347 a.a. *
Ligands
NAD ×4
SO4 ×10
Waters ×491
* Residue conservation analysis
PDB id:
3gfb
Name: Oxidoreductase
Title: L-threonine dehydrogenase (tktdh) from the hyperthermophilic archaeon thermococcus kodakaraensis
Structure: L-threonine 3-dehydrogenase. Chain: a, b, c, d. Engineered: yes
Source: Thermococcus kodakarensis. Organism_taxid: 69014. Gene: tdh, tk0916. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.220     R-free:   0.277
Authors: A.Bowyer
Key ref: A.Bowyer et al. (2009). Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Struct Biol, 168, 294-304. PubMed id: 19616102 DOI: 10.1016/j.jsb.2009.07.011
Date:
26-Feb-09     Release date:   06-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5JI69  (TDH_PYRKO) -  Probable L-threonine 3-dehydrogenase
Seq:
Struc:
350 a.a.
347 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.103  - L-threonine 3-dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-threonine + NAD+ = L-2-amino-3-oxobutanoate + NADH
L-threonine
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= L-2-amino-3-oxobutanoate
+ 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     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jsb.2009.07.011 J Struct Biol 168:294-304 (2009)
PubMed id: 19616102  
 
 
Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis.
A.Bowyer, H.Mikolajek, J.W.Stuart, S.P.Wood, F.Jamil, N.Rashid, M.Akhtar, J.B.Cooper.
 
  ABSTRACT  
 
The X-ray structure of the holo-form of l-threonine dehydrogenase (TDH) from Thermococcus kodakaraensis (TkTDH) has been determined at 2.4A resolution. TDH catalyses the NAD(+)-dependent oxidation of l-threonine to 2-amino-3-ketobutyrate, and is one of the first enzymes in this family to be solved by X-ray crystallography. The enzyme is a homo-tetramer, each monomer consisting of 350 amino acids that form two domains; a catalytic domain and a nicotinamide co-factor (NAD(+))-binding domain, which contains an alpha/beta Rossmann fold motif. An extended twelve-stranded beta-sheet is formed by the association of pairs of monomers in the tetramer. TkTDH shows strong overall structural similarity to TDHs from thermophiles and alcohol dehydrogenases (ADH) from lower life forms, despite low sequence homology, exhibiting the same overall fold of the monomer and assembly of the tetramer. The structure reveals the binding site of the essential co-factor NAD(+) which is present in all subunits. Docking studies suggest a mode of interaction of TDH with 2-amino-3-ketobutyrate CoA ligase, the subsequent enzyme in the pathway for conversion of threonine to glycine. TDH is known to form a stable functional complex with 2-amino-3-ketobutyrate ligase, most probably to shield an unstable intermediate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21078123 K.Yoneda, H.Sakuraba, I.Muraoka, T.Oikawa, and T.Ohshima (2010).
Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily.
  FEBS J, 277, 5124-5132.
PDB code: 2yy7
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