mouse TDH in the apo form

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Structural insights on mouse l-threonine dehydrogenase: A regulatory role of Arg180 in catalysis

He, C.Huang, X.Liu, Y.Li, F.Yang, Y.Tao, H.Han, C.Zhao, C.Xiao, Y.Shi, Y.

(2015) J Struct Biol 192: 510-518

  • DOI: https://doi.org/10.1016/j.jsb.2015.10.014
  • Primary Citation of Related Structures:  
    4YR9, 4YRA, 4YRB

  • PubMed Abstract: 

    Mouse L-threonine dehydrogenase (mTDH), which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and mediates threonine catabolism, plays pivotal roles in both powerful biosynthesis and signaling in mouse stem cells and has a regulatory residue Arg180. Here we determined three crystal structures of mTDH: wild-type (WT) in the apo form; in complex with NAD(+) and a substrate analog, glycerol, or with only NAD(+); as well as the R180K variant with NAD(+). This is the first description of a structure for mammalian SDR-type TDH. Structural comparison revealed the structural basis for SDR-type TDH catalysis remains strictly conserved in bacteria and mammals. Kinetic enzyme assays, and isothermal titration calorimetry (ITC) measurements indicated the R180K mutation has little effect on NAD(+) binding affinity, whereas affects the substrate's affinity for the enzyme. The crystal structure of R180K with NAD(+), biochemical and spectroscopic studies suggested that the R180K mutant should bind NAD(+) in a similar way and have a similar folding to the WT. However, the R180K variant may have difficulty adopting the closed form due to reduced interaction of residue 180 with a loop which connects a key position for mTDH switching between the closed and open forms in mTDH catalysis, and thereby exhibited a significantly decreased kcat/Km value toward the substrate, L-Thr. In sum, our results suggest that activity of GalE-like TDH can be regulated by remote interaction, such as hydrogen bonding and hydrophobic interaction around the Arg180 of mTDH.

  • Organizational Affiliation

    Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China. Electronic address: chaohe@ahu.edu.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-threonine 3-dehydrogenase, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
329Mus musculusMutation(s): 0 
Gene Names: Tdh
Find proteins for Q8K3F7 (Mus musculus)
Explore Q8K3F7 
Go to UniProtKB:  Q8K3F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K3F7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.445α = 90
b = 157.31β = 97
c = 162.336γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2016-02-03 
  • Deposition Author(s): He, C., Li, F.

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description