spacer
spacer

PDBsum entry 1y7t

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1y7t
Jmol
Contents
Protein chains
327 a.a. *
Ligands
NDP ×2
TRS ×4
Waters ×434
* Residue conservation analysis
PDB id:
1y7t
Name: Oxidoreductase
Title: Crystal structure of NAD(h)-depenent malate dehydrogenase complexed with NADPH
Structure: Malate dehydrogenase. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Strain: at-62. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.65Å     R-factor:   0.197     R-free:   0.207
Authors: T.Tomita,S.Fushinobu,T.Kuzuyama,M.Nishiyama
Key ref: T.Tomita et al. (2005). Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H). Biochem Biophys Res Commun, 334, 613-618. PubMed id: 16009341 DOI: 10.1016/j.bbrc.2005.06.133
Date:
10-Dec-04     Release date:   02-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10584  (MDH_THETH) -  Malate dehydrogenase
Seq:
Struc:
327 a.a.
327 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.37  - Malate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: (S)-malate + NAD+ = oxaloacetate + NADH
(S)-malate
Bound ligand (Het Group name = TRS)
matches with 41.00% similarity
+
NAD(+)
Bound ligand (Het Group name = NDP)
matches with 91.00% similarity
= oxaloacetate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.bbrc.2005.06.133 Biochem Biophys Res Commun 334:613-618 (2005)
PubMed id: 16009341  
 
 
Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H).
T.Tomita, S.Fushinobu, T.Kuzuyama, M.Nishiyama.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20845078 Z.D.Wang, B.J.Wang, Y.D.Ge, W.Pan, J.Wang, L.Xu, A.M.Liu, and G.P.Zhu (2011).
Expression and identification of a thermostable malate dehydrogenase from multicellular prokaryote Streptomyces avermitilis MA-4680.
  Mol Biol Rep, 38, 1629-1636.  
16960374 T.Tomita, T.Kuzuyama, and M.Nishiyama (2006).
Alteration of coenzyme specificity of lactate dehydrogenase from Thermus thermophilus by introducing the loop region of NADP(H)-dependent malate dehydrogenase.
  Biosci Biotechnol Biochem, 70, 2230-2235.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.