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PDBsum entry 2x0i

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protein ligands metals links
Oxidoreductase PDB id
2x0i
Jmol
Contents
Protein chain
294 a.a. *
Ligands
NAI
SO4
Metals
_NA
Waters ×39
* Residue conservation analysis
PDB id:
2x0i
Name: Oxidoreductase
Title: 2.9 a resolution structure of malate dehydrogenase from archaeoglobus fulgidus in complex with nadh
Structure: Malate dehydrogenase. Chain: a. Engineered: yes
Source: Archaeoglobus fulgidus dsm 4304. Organism_taxid: 224325. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.91Å     R-factor:   0.155     R-free:   0.218
Authors: A.Irimia,D.Madern,G.Zaccai,F.M.D.Vellieux,A.Karshikoff,G.Tib R.Ladenstein,T.Lien,N.-K.Birkeland
Key ref:
A.Irimia et al. (2004). The 2.9A resolution crystal structure of malate dehydrogenase from Archaeoglobus fulgidus: mechanisms of oligomerisation and thermal stabilisation. J Mol Biol, 335, 343-356. PubMed id: 14659762 DOI: 10.1016/j.jmb.2003.10.054
Date:
14-Dec-09     Release date:   22-Dec-09    
Supersedes: 1ojs
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O08349  (MDH_ARCFU) -  Malate dehydrogenase
Seq:
Struc:
294 a.a.
294 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
+
NAD(+)
Bound ligand (Het Group name = NAI)
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   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2003.10.054 J Mol Biol 335:343-356 (2004)
PubMed id: 14659762  
 
 
The 2.9A resolution crystal structure of malate dehydrogenase from Archaeoglobus fulgidus: mechanisms of oligomerisation and thermal stabilisation.
A.Irimia, F.M.Vellieux, D.Madern, G.Zaccaï, A.Karshikoff, G.Tibbelin, R.Ladenstein, T.Lien, N.K.Birkeland.
 
  ABSTRACT  
 
The crystal structure of malate dehydrogenase from the hyperthermophilic archaeon Archeoglobus fulgidus, in complex with its cofactor NAD, was solved at 2.9A resolution. The crystal structure shows a compact homodimer with one coenzyme bound per subunit. The substrate binding site is occupied by a sulphate ion. In order to gain insight into adaptation mechanisms, which allow the protein to be stable and active at high temperatures, the 3D structure was compared to those of several thermostable and hyperthermostable homologues, and to halophilic malate dehydrogenase. The hyperthermostable A. fulgidus MalDH protein displays a reduction of the solvent-exposed surface, an optimised compact hydrophobic core, a high number of hydrogen bonds, and includes a large number of ion pairs at the protein surface. These features occur concomitantly with a reduced number of residues in the protein subunit, due to several deletions in loop regions. The loops are further stiffened by ion pair links with secondary structure elements. A. fulgidus malate dehydrogenase is the only MalDH family. All the other known members of this family are homo-tetramers. The crystal structures revealed that the association of the dimers to form tetramers is prevented by several deletions, taking place at the level of two loops that are known to be essential for the tetramerisation process within the LDH and MalDH enzymes.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. View of the AfMalDH dimer, showing the distribution of the average temperature factors for one of the subunits: the colouring for monomer A is representative of the range of temperature factors, from the lowest values (ca 33.0 Å2) in dark blue to the highest values (ca 99.0 Å2) in red. For clarity, monomer B is shown in translucent grey, and the two subunits are equal due to crystallographic symmetry. Arrows indicate the mobile loops that cover the active sites.
Figure 5.
Figure 5. Structural differences between the subunits of AfMalDH, HmMalDH (both belonging to the (LDH-like) MalDH family), TmLDH and AaMalDH. Each subunit is represented by its C^a trace, with the AfMalDH subunit always shown by the thickest lines. The regions indicated by arrows correspond to the loops where deletions are found. Residue numbers are indicated with the linear numbering scheme. (a) Superimposed subunits of AfMalDH, HmMalDH (thin lines) and TmLDH (broken lines); (b) superimposed subunits of AfMalDH and AaMalDH (thin lines).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 343-356) copyright 2004.  
  Figures were selected by the author.  

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.  
17487443 L.J.Yennaco, Y.Hu, and J.F.Holden (2007).
Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum.
  Extremophiles, 11, 741-746.  
17683333 M.Tehei, and G.Zaccai (2007).
Adaptation to high temperatures through macromolecular dynamics by neutron scattering.
  FEBS J, 274, 4034-4043.  
16868745 M.Tehei, R.Daniel, and G.Zaccai (2006).
Fundamental and biotechnological applications of neutron scattering measurements for macromolecular dynamics.
  Eur Biophys J, 35, 551-558.  
16945919 S.Hara, K.Motohashi, F.Arisaka, P.G.Romano, N.Hosoya-Matsuda, N.Kikuchi, N.Fusada, and T.Hisabori (2006).
Thioredoxin-h1 reduces and reactivates the oxidized cytosolic malate dehydrogenase dimer in higher plants.
  J Biol Chem, 281, 32065-32071.  
16266275 A.T.Eprintsev, M.I.Falaleeva, and N.V.Parfyonova (2005).
Malate dehydrogenase from the thermophilic bacterium Vulcanithermus medioatlanticus.
  Biochemistry (Mosc), 70, 1027-1030.  
16203729 M.Tehei, D.Madern, B.Franzetti, and G.Zaccai (2005).
Neutron scattering reveals the dynamic basis of protein adaptation to extreme temperature.
  J Biol Chem, 280, 40974-40979.  
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.  
15265031 A.P.Maloney, S.M.Callan, P.G.Murray, and M.G.Tuohy (2004).
Mitochondrial malate dehydrogenase from the thermophilic, filamentous fungus Talaromyces emersonii.
  Eur J Biochem, 271, 3115-3126.  
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.