1Y7T

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

• PDB DOI: https://doi.org/10.2210/pdb1Y7T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-10 Released: 2005-08-02 
• Deposition Author(s): Tomita, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

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Experimental Data Snapshot

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

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

• PubMed: 16009341 
• DOI: https://doi.org/10.1016/j.bbrc.2005.06.133
• Primary Citation of Related Structures:  
  1Y7T, 2CVQ


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.91 kDa 
• Atom Count: 5,540 
• Modelled Residue Count: 654 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	327	Thermus thermophilus	Mutation(s): 0  EC: 1.1.1.37
UniProt
Find proteins for P10584 (Thermus thermophilus) Explore P10584  Go to UniProtKB:  P10584

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TRS	D [auth A], E [auth A], G [auth B], H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.207 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.12	α = 90
b = 85.17	β = 90
c = 117.93	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-02 
Deposition Author(s): Tomita, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations