4KDF

Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.356 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.

Hung, C.H.Hwang, T.S.Chang, Y.Y.Luo, H.R.Wu, S.P.Hsu, C.H.

(2013) Plos One 8: e83091-e83091

  • DOI: 10.1371/journal.pone.0083091
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in thera ...

    Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60 °C and specific activity of about 2,600 U/mg with optimal temperature of 90 °C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity.


    Organizational Affiliation

    Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan.,Department of Biotechnology, Yuanpei University, Hsinchu, Taiwan.,Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan ; Genome and Systems Biology Degree Program; Center for Systems Biology, National Taiwan University, Taipei, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
A, B, C, D
341Thermus thermophilusMutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for P10584 (Thermus thermophilus)
Go to UniProtKB:  P10584
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.356 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.601α = 90.00
b = 114.617β = 90.00
c = 144.077γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
HKL-2000data collection
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release