Crystal structure of thermolabile L-threonine dehydrogenase from Flavobacterium frigidimaris KUC-1

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.195 

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Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily

Yoneda, K.Sakuraba, H.Muraoka, I.Oikawa, T.Ohshima, T.

(2010) FEBS J 277: 5124-5132

  • DOI: https://doi.org/10.1111/j.1742-4658.2010.07916.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of a L-threonine dehydrogenase (L-ThrDH; EC from the psychrophilic bacterium Flavobacterium frigidimaris KUC-1, which shows no sequence similarity to conventional L-ThrDHs, was determined in the presence of NAD and a substrate analog, glycerol. The asymmetric unit consisted of two subunits related by a two-fold rotation axis. Each monomer consisted of a Rossmann-fold domain and a carboxyl-terminal catalytic domain. The overall fold of F. frigidimaris L-ThrDH showed significant similarity to that of UDP-galactose 4-epimerase (GalE); however, structural comparison of the enzyme with E. coli and human GalEs showed clear topological differences in three loops (loop 1, loop 2 and the NAD-binding loop) around the substrate and NAD binding sites. In F. frigidimaris L-ThrDH, loops 1 and 2 insert toward the active site cavity, creating a barrier preventing the binding of UDP-glucose. Alternatively, loop 1 contributes to a unique substrate binding pocket in the F. frigidimaris enzyme. The NAD binding loop, which tightly holds the adenine ribose moiety of NAD in the Escherichia coli and human GalEs, is absent in F. frigidimaris L-ThrDH. Consequently, the cofactor binds to F. frigidimaris L-ThrDH in a reversible manner, unlike its binding to GalE. The substrate binding model suggests that the reaction proceeds through abstraction of the β-hydroxyl hydrogen of L-threonine via either a proton shuttle mechanism driven by Tyr143 and facilitated by Ser118 or direct proton transfer driven by Tyr143. The present structure provides a clear bench mark for distinguishing GalE-like L-ThrDHs from GalEs.

  • Organizational Affiliation

    Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-threonine dehydrogenase
A, B
312Flavobacterium frigidimarisMutation(s): 0 
Gene Names: ltd
Find proteins for Q8KZM4 (Flavobacterium frigidimaris)
Explore Q8KZM4 
Go to UniProtKB:  Q8KZM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KZM4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
C21 H27 N7 O14 P2
Query on PE8

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C [auth A],
D [auth A],
H [auth B],
I [auth B]
C16 H34 O9
Query on MES

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F [auth A],
K [auth B]
C6 H13 N O4 S
Query on GOL

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G [auth A],
L [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.029α = 90
b = 88.142β = 90
c = 123.944γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance