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PDBsum entry 2mdh

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Oxidoreductase(NAD(a)-choh(d)) PDB id
2mdh
Jmol
Contents
Protein chains
324 a.a.
325 a.a.
Ligands
NAD ×2
SUL ×2
Superseded by: 4mdh
PDB id:
2mdh
Name: Oxidoreductase(NAD(a)-choh(d))
Structure: Cytoplasmic malate dehydrogenase
Source: Porcine (sus scrofa) heart
Authors: J.J.Birktoft,L.J.Banaszak
Key ref: J.J.Birktoft and L.J.Banaszak (1983). The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase. J Biol Chem, 258, 472-482. PubMed id: 6848515
Date:
15-Mar-83     Release date:   21-Apr-83    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 324 a.a.
Protein chain
No UniProt id for this chain
Struc: 325 a.a.
Key:    Secondary structure  CATH domain

 

 
J Biol Chem 258:472-482 (1983)
PubMed id: 6848515  
 
 
The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase.
J.J.Birktoft, L.J.Banaszak.
 
  ABSTRACT  
 
The structure of cytoplasmic malate dehydrogenase has been partially refined by crystallographic least squares methods. Using x-ray phases based on the refined coordinates, analysis of the resultant electron density maps has led to a new model of cytoplasmic malate dehydrogenase and a tentative "x-ray sequence." The two crystallographically independent subunits comprising the dimeric enzyme are nearly identical in structure and are related to each other by roughly 2-fold rotational symmetry. The best fit of the molecular structure of cytoplasmic malate dehydrogenase to that of lactate dehydrogenase has been obtained by least squares methods. The active sites of these two enzymes contain similarly oriented His-Asp pairs linked by a hydrogen bond which may function as a proton relay system during catalysis. This pair could also provide an explanation for the relatively stronger binding by cytoplasmic malate dehydrogenase and lactate dehydrogenase of NADH versus NAD. Similar His-Asp pairs have been observed in the serine proteases, thermolysin, and phospholipase A2, and the His-Asp pair may play a similar functional role in all of these enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19229245 S.M.Lee, J.H.Kim, E.J.Cho, and H.D.Youn (2009).
A nucleocytoplasmic malate dehydrogenase regulates p53 transcriptional activity in response to metabolic stress.
  Cell Death Differ, 16, 738-748.  
15206932 V.Ali, T.Hashimoto, Y.Shigeta, and T.Nozaki (2004).
Molecular and biochemical characterization of D-phosphoglycerate dehydrogenase from Entamoeba histolytica. A unique enteric protozoan parasite that possesses both phosphorylated and nonphosphorylated serine metabolic pathways.
  Eur J Biochem, 271, 2670-2681.  
11155166 S.Kawabata, Y.Terao, and S.Hamada (2000).
Molecular cloning, sequence and characterization of a novel streptococcal phosphoglycerate dehydrogenase gene.
  Oral Microbiol Immunol, 15, 58-62.  
10079073 K.L.Turner, M.K.Doherty, H.A.Heering, F.A.Armstrong, G.A.Reid, and S.K.Chapman (1999).
Redox properties of flavocytochrome c3 from Shewanella frigidimarina NCIMB400.
  Biochemistry, 38, 3302-3309.  
10583384 M.C.Cazzulo Franke, J.Vernal, J.J.Cazzulo, and C.Nowicki (1999).
The NAD-linked aromatic alpha-hydroxy acid dehydrogenase from Trypanosoma cruzi. A new member of the cytosolic malate dehydrogenases group without malate dehydrogenase activity.
  Eur J Biochem, 266, 903-910.  
10477256 Y.Xu, G.Bhargava, H.Wu, G.Loeber, and L.Tong (1999).
Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme: a new class of oxidative decarboxylases.
  Structure, 7, R877-R889.  
9692968 M.A.Jairajpuri, N.Azam, K.Baburaj, E.Bulliraju, and S.Durani (1998).
Charge and solvation effects in anion recognition centers: an inquiry exploiting reactive arginines.
  Biochemistry, 37, 10780-10791.  
9485426 M.S.Cosgrove, C.Naylor, S.Paludan, M.J.Adams, and H.R.Levy (1998).
On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase.
  Biochemistry, 37, 2759-2767.
PDB code: 2dpg
9665169 P.J.Baker, Y.Sawa, H.Shibata, S.E.Sedelnikova, and D.W.Rice (1998).
Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.
  Nat Struct Biol, 5, 561-567.
PDB codes: 1pjb 1pjc 1say
8993342 X.Y.He, H.Deng, and S.Y.Yang (1997).
Importance of the gamma-carboxyl group of glutamate-462 of the large alpha-subunit for the catalytic function and the stability of the multienzyme complex of fatty acid oxidation from Escherichia coli.
  Biochemistry, 36, 261-268.  
8665917 M.Lemaire, M.Miginiac-Maslow, and P.Decottignies (1996).
The catalytic site of chloroplastic NADP-dependent malate dehydrogenase contains a His/Asp pair.
  Eur J Biochem, 236, 947-952.  
8994968 R.L.Kingston, R.K.Scopes, and E.N.Baker (1996).
The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP.
  Structure, 4, 1413-1428.
PDB code: 1ofg
8639525 S.L.Schafer, W.C.Barrett, A.T.Kallarakal, B.Mitra, J.W.Kozarich, J.A.Gerlt, J.G.Clifton, G.A.Petsko, and G.L.Kenyon (1996).
Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant.
  Biochemistry, 35, 5662-5669.
PDB code: 1mra
8755745 X.Y.He, and S.Y.Yang (1996).
Histidine-450 is the catalytic residue of L-3-hydroxyacyl coenzyme A dehydrogenase associated with the large alpha-subunit of the multienzyme complex of fatty acid oxidation from Escherichia coli.
  Biochemistry, 35, 9625-9630.  
7719856 D.J.Schuller, G.A.Grant, and L.J.Banaszak (1995).
The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
  Nat Struct Biol, 2, 69-76.
PDB code: 1psd
8749373 V.S.Lamzin, Z.Dauter, and K.S.Wilson (1995).
How nature deals with stereoisomers.
  Curr Opin Struct Biol, 5, 830-836.  
  7849603 C.R.Goward, and D.J.Nicholls (1994).
Malate dehydrogenase: a model for structure, evolution, and catalysis.
  Protein Sci, 3, 1883-1888.  
7664032 V.S.Lamzin, Z.Dauter, and K.S.Wilson (1994).
Dehydrogenation through the looking-glass.
  Nat Struct Biol, 1, 281-282.  
8444183 D.J.Nicholls, I.S.Wood, T.J.Nobbs, A.R.Clarke, J.J.Holbrook, T.Atkinson, and M.D.Scawen (1993).
Dissecting the contributions of a specific side-chain interaction to folding and catalysis of Bacillus stearothermophilus lactate dehydrogenase.
  Eur J Biochem, 212, 447-455.  
  1735722 C.Charnock, U.H.Refseth, and R.Sirevåg (1992).
Malate dehydrogenase from Chlorobium vibrioforme, Chlorobium tepidum, and Heliobacterium gestii: purification, characterization, and investigation of dinucleotide binding by dehydrogenases by use of empirical methods of protein sequence analysis.
  J Bacteriol, 174, 1307-1313.  
1541275 C.Prodromou, P.J.Artymiuk, and J.R.Guest (1992).
The aconitase of Escherichia coli. Nucleotide sequence of the aconitase gene and amino acid sequence similarity with mitochondrial aconitases, the iron-responsive-element-binding protein and isopropylmalate isomerases.
  Eur J Biochem, 204, 599-609.  
  1338973 F.Lederer (1992).
Extreme pKa displacements at the active sites of FMN-dependent alpha-hydroxy acid-oxidizing enzymes.
  Protein Sci, 1, 540-548.  
  1986231 K.I.Minard, and L.McAlister-Henn (1991).
Isolation, nucleotide sequence analysis, and disruption of the MDH2 gene from Saccharomyces cerevisiae: evidence for three isozymes of yeast malate dehydrogenase.
  Mol Cell Biol, 11, 370-380.  
2209586 C.Crétin, P.Luchetta, C.Joly, P.Decottignies, L.Lepiniec, P.Gadal, M.Sallantin, J.C.Huet, and J.C.Pernollet (1990).
Primary structure of sorghum malate dehydrogenase (NADP) deduced from cDNA sequence. Homology with malate dehydrogenase (NAD).
  Eur J Biochem, 192, 299-303.  
2377615 C.Gietl (1990).
Glyoxysomal malate dehydrogenase from watermelon is synthesized with an amino-terminal transit peptide.
  Proc Natl Acad Sci U S A, 87, 5773-5777.  
2110059 E.Honka, S.Fabry, T.Niermann, P.Palm, and R.Hensel (1990).
Properties and primary structure of the L-malate dehydrogenase from the extremely thermophilic archaebacterium Methanothermus fervidus.
  Eur J Biochem, 188, 623-632.  
2798408 A.H.Robbins, and C.D.Stout (1989).
The structure of aconitase.
  Proteins, 5, 289-312.  
2658216 A.R.Clarke, T.Atkinson, and J.J.Holbrook (1989).
From analysis to synthesis: new ligand binding sites on the lactate dehydrogenase framework. Part I.
  Trends Biochem Sci, 14, 101-105.  
  2681152 P.V.Schoenlein, B.B.Roa, and M.E.Winkler (1989).
Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12.
  J Bacteriol, 171, 6084-6092.  
  3233689 C.Queiroz-Claret, C.Valon, and O.Queiroz (1988).
Are spontaneous conformational interconversions a molecular basis for long-period oscillations in enzyme activity?
  Chronobiol Int, 5, 301-309.  
3076279 L.McAlister-Henn (1988).
Evolutionary relationships among the malate dehydrogenases.
  Trends Biochem Sci, 13, 178-181.  
3479790 J.J.Birktoft, H.M.Holden, R.Hamlin, N.H.Xuong, and L.J.Banaszak (1987).
Structure of L-3-hydroxyacyl-coenzyme A dehydrogenase: preliminary chain tracing at 2.8-A resolution.
  Proc Natl Acad Sci U S A, 84, 8262-8266.  
3665938 K.Fickenscher, R.Scheibe, and F.Marcus (1987).
Amino acid sequence similarity between malate dehydrogenases (NAD) and pea chloroplast malate dehydrogenase (NADP).
  Eur J Biochem, 168, 653-658.  
  3312168 L.McAlister-Henn, and L.M.Thompson (1987).
Isolation and expression of the gene encoding yeast mitochondrial malate dehydrogenase.
  J Bacteriol, 169, 5157-5166.  
3322223 R.F.Vogel, K.D.Entian, and D.Mecke (1987).
Cloning and sequence of the mdh structural gene of Escherichia coli coding for malate dehydrogenase.
  Arch Microbiol, 149, 36-42.  
2992968 K.G.Welinder (1985).
Plant peroxidases. Their primary, secondary and tertiary structures, and relation to cytochrome c peroxidase.
  Eur J Biochem, 151, 497-504.  
  2993232 P.Sutherland, and L.McAlister-Henn (1985).
Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase.
  J Bacteriol, 163, 1074-1079.  
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 code is shown on the right.