4YRB

mouse TDH mutant R180K with NAD+ bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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Literature

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: 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 ...

    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: 

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-threonine 3-dehydrogenase, mitochondrial
A, B, C, D, E, F
A, B, C, D, E, F
329Mus musculusMutation(s): 1 
Gene Names: Tdh
EC: 1.1.1.103
UniProt
Find proteins for Q8K3F7 (Mus musculus)
Explore Q8K3F7 
Go to UniProtKB:  Q8K3F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K3F7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
G [auth A],
H [auth B],
I [auth C],
J [auth D],
K [auth E],
L [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.24α = 90
b = 154.05β = 90
c = 199.19γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-03-14 
  • 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