3GFB

L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis

Bowyer, A.Mikolajek, H.Stuart, J.W.Wood, S.P.Jamil, F.Rashid, N.Akhtar, M.Cooper, J.B.

(2009) J.Struct.Biol. 168: 294-304

  • DOI: 10.1016/j.jsb.2009.07.011

  • PubMed 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 ...

    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.


    Organizational Affiliation

    University of Southampton, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-threonine 3-dehydrogenase
A, B, C, D
350Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
Gene Names: tdh
EC: 1.1.1.103
Find proteins for Q5JI69 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q5JI69
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 2.4 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.481α = 90.00
b = 124.481β = 90.00
c = 271.143γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-26 
  • Released Date: 2009-10-06 
  • Deposition Author(s): Bowyer, A.

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance