1Y7T

Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H)

Tomita, T.Fushinobu, S.Kuzuyama, T.Nishiyama, M.

(2005) Biochem.Biophys.Res.Commun. 334: 613-618

  • DOI: 10.1016/j.bbrc.2005.06.133
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For better understanding of the coenzyme specificity in NAD-dependent MDH (tMDH) from Thermus flavus AT-62, we determined the crystal structures of tMDH-NADP(H) complex at maximally 1.65 A resolution. The overall structure is almost the same as that ...

    For better understanding of the coenzyme specificity in NAD-dependent MDH (tMDH) from Thermus flavus AT-62, we determined the crystal structures of tMDH-NADP(H) complex at maximally 1.65 A resolution. The overall structure is almost the same as that of the tMDH-NADH complex. However, NADP(H) binds to tMDH in the reverse orientation, where adenine occupies the position near the catalytic center and nicotinamide is positioned at the adenine binding site of the tMDH-NADH complex. Consistent with this, kinetic analysis of the malate-oxidizing reaction revealed that NADP(+) inhibited tMDH at high concentrations. This has provided the first evidence for the alternative binding mode of the nicotinamide coenzyme, that has pseudo-symmetry in its structure, in a single enzyme.


    Related Citations: 
    • Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution
      Birktoft, J.J.,Rhodes, G.,Banaszak, L.J.
      (1989) Biochemistry 28: 6065
    • Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity
      Nishiyama, M.,Matsubara, N.,Yamamoto, K.,Iijima, S.,Uozumi, T.,Beppu, T.
      (1986) J.Biol.Chem. 261: 14178
    • Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus
      Kelly, C.A.,Nishiyama, M.,Ohnishi, Y.,Beppu, T.,Birktoft, J.J.
      (1993) Biochemistry 32: 3913
    • Preliminary X-ray diffraction analysis of a crystallizable mutant of malate dehydrogenase from the thermophile Thermus flavus
      Kelly, C.A.,Sarfaty, S.,Nishiyama, M.,Beppu, T.,Birktoft, J.J.
      (1991) J.Mol.Biol. 221: 383
    • The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase
      Birktoft, J.J.,Banaszak, L.J.
      (1983) J.Biol.Chem. 258: 472
    • Malate Dehydrogenases
      Banaszak, L.J.,Bradshaw, R.A.
      (1975) Enzyme 11: 369


    Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
A, B
327Thermus thermophilusMutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for P10584 (Thermus thermophilus)
Go to UniProtKB:  P10584
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.120α = 90.00
b = 85.170β = 90.00
c = 117.930γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance