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PDBsum entry 5mdh

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
5mdh
Jmol
Contents
Protein chains
333 a.a. *
Ligands
NAD ×2
MAK ×2
Waters ×354
* Residue conservation analysis
PDB id:
5mdh
Name: Oxidoreductase
Title: Crystal structure of ternary complex of porcine cytoplasmic dehydrogenase alpha-ketomalonate and tnad at 2.4 angstroms
Structure: Malate dehydrogenase. Chain: a, b. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: heart. Tissue: muscle. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.199     R-free:   0.253
Authors: A.D.M.Chapman,A.Cortes,T.R.Dafforn,A.R.Clarke,R.L.Brady
Key ref:
A.D.Chapman et al. (1999). Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD. J Mol Biol, 285, 703-712. PubMed id: 10075524 DOI: 10.1006/jmbi.1998.2357
Date:
08-Oct-98     Release date:   18-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11708  (MDHC_PIG) -  Malate dehydrogenase, cytoplasmic
Seq:
Struc:
334 a.a.
333 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 = MAK)
matches with 54.55% similarity
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= oxaloacetate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.2357 J Mol Biol 285:703-712 (1999)
PubMed id: 10075524  
 
 
Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.
A.D.Chapman, A.Cortés, T.R.Dafforn, A.R.Clarke, R.L.Brady.
 
  ABSTRACT  
 
The structural basis for the extreme discrimination achieved by malate dehydrogenases between a variety of closely related substrates encountered within the cell has been difficult to assess because of the lack of an appropriate catalytically competent structure of the enzyme. Here, we have determined the crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase with the alternative substrate alpha-ketomalonate and the coenzyme analogue 1,4,5,6-tetrahydronicotinamide. Both subunits of the dimeric porcine heart, and from the prokaryotes Escherichia coli and Thermus flavus. However, large changes are noted around the active site, where a mobile loop now closes to bring key residues into contact with the substrate. This observation substantiates a postulated mechanism in which the enzyme achieves high levels of substrate discrimination through charge balancing in the active site. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by a conserved arginine in the active site loop. The enzyme must, however, also discriminate against smaller substrates, such as pyruvate. The structure shows in the closed (loop down) catalytically competent complex two arginine residues (91 and 97) are driven into close proximity. Without the complimentary, negative charge of the substrate side-chain of oxaloacetate or alpha-ketomalonate, charge repulsion would resist formation production of this catalytically productive conformation, hence minimising the effectiveness of pyruvate as a substrate. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. The position of the α-ketomalonate substrate within the active site. The electron density was generated by calculating 2|F[obs]|−|F[calc]| difference maps contoured at 1.3σ.
Figure 8.
Figure 8. The hydrogen-bonding interactions of α-ketomalonate with the key active site residues. This Figure was generated using the program LIGPLOT [Wallace et al 1995].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 703-712) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20852941 H.Xia, C.Wu, Q.Xu, J.Shi, F.Feng, K.Chen, Q.Yao, Y.Wang, and L.Wang (2011).
Molecular cloning and characterization of lactate dehydrogenase gene 1 in the silkworm, Bombyx mori.
  Mol Biol Rep, 38, 1853-1860.  
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.  
21114258 J.D.Keighron, and C.D.Keating (2010).
Enzyme:nanoparticle bioconjugates with two sequential enzymes: stoichiometry and activity of malate dehydrogenase and citrate synthase on Au nanoparticles.
  Langmuir, 26, 18992-19000.  
19184366 A.Pradhan, P.Mukherjee, A.K.Tripathi, M.A.Avery, L.A.Walker, and B.L.Tekwani (2009).
Analysis of quaternary structure of a [LDH-like] malate dehydrogenase of Plasmodium falciparum with oligomeric mutants.
  Mol Cell Biochem, 325, 141-148.  
16541263 N.Zheng, B.Huang, J.Xu, S.Huang, J.Chen, X.Hu, K.Ying, and X.Yu (2006).
Enzymatic and physico-chemical characteristics of recombinant cMDH and mMDH of Clonorchis sinensis.
  Parasitol Res, 99, 174-180.  
15670147 B.Cox, M.M.Chit, T.Weaver, C.Gietl, J.Bailey, E.Bell, and L.Banaszak (2005).
Organelle and translocatable forms of glyoxysomal malate dehydrogenase. The effect of the N-terminal presequence.
  FEBS J, 272, 643-654.
PDB codes: 1sev 1smk
15117937 A.Cameron, J.Read, R.Tranter, V.J.Winter, R.B.Sessions, R.L.Brady, L.Vivas, A.Easton, H.Kendrick, S.L.Croft, D.Barros, J.L.Lavandera, J.J.Martin, F.Risco, S.García-Ochoa, F.J.Gamo, L.Sanz, L.Leon, J.R.Ruiz, R.Gabarró, A.Mallo, and F.Gómez de las Heras (2004).
Identification and activity of a series of azole-based compounds with lactate dehydrogenase-directed anti-malarial activity.
  J Biol Chem, 279, 31429-31439.
PDB codes: 1t24 1t25 1t26 1t2c 1t2d 1t2e 1t2f
15317584 A.K.Tripathi, P.V.Desai, A.Pradhan, S.I.Khan, M.A.Avery, L.A.Walker, and B.L.Tekwani (2004).
An alpha-proteobacterial type malate dehydrogenase may complement LDH function in Plasmodium falciparum. Cloning and biochemical characterization of the enzyme.
  Eur J Biochem, 271, 3488-3502.  
12588867 J.A.Lodge, T.Maier, W.Liebl, V.Hoffmann, and N.Sträter (2003).
Crystal structure of Thermotoga maritima alpha-glucosidase AglA defines a new clan of NAD+-dependent glycosidases.
  J Biol Chem, 278, 19151-19158.
PDB code: 1obb
11276087 J.A.Read, V.J.Winter, C.M.Eszes, R.B.Sessions, and R.L.Brady (2001).
Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase.
  Proteins, 43, 175-185.
PDB codes: 1i0z 1i10
10998181 D.Madern (2000).
The putative L-lactate dehydrogenase from Methanococcus jannaschii is an NADPH-dependent L-malate dehydrogenase.
  Mol Microbiol, 37, 1515-1520.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.