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PDBsum entry 1gv1

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
1gv1
Jmol
Contents
Protein chains
305 a.a. *
290 a.a. *
Waters ×450
* Residue conservation analysis
PDB id:
1gv1
Name: Oxidoreductase
Title: Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases
Structure: Malate dehydrogenase. Chain: a, b, c, d. Engineered: yes
Source: Chlorobium vibrioforme. Organism_taxid: 1098. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.5Å     R-factor:   0.216     R-free:   0.305
Authors: B.Dalhus,M.Sarinen,U.H.Sauer,P.Eklund,K.Johansson, A.Karlsson,S.Ramaswamy,A.Bjork,B.Synstad,K.Naterstad, R.Sirevag,H.Eklund
Key ref:
B.Dalhus et al. (2002). Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases. J Mol Biol, 318, 707-721. PubMed id: 12054817 DOI: 10.1016/S0022-2836(02)00050-5
Date:
04-Feb-02     Release date:   20-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0C890  (MDH_CHLVI) -  Malate dehydrogenase
Seq:
Struc:
310 a.a.
305 a.a.*
Protein chains
Pfam   ArchSchema ?
P0C890  (MDH_CHLVI) -  Malate dehydrogenase
Seq:
Struc:
310 a.a.
290 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: 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(+)
= 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     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00050-5 J Mol Biol 318:707-721 (2002)
PubMed id: 12054817  
 
 
Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases.
B.Dalhus, M.Saarinen, U.H.Sauer, P.Eklund, K.Johansson, A.Karlsson, S.Ramaswamy, A.Bjørk, B.Synstad, K.Naterstad, R.Sirevåg, H.Eklund.
 
  ABSTRACT  
 
The three-dimensional structure of four malate dehydrogenases (MDH) from thermophilic and mesophilic phototropic bacteria have been determined by X-ray crystallography and the corresponding structures compared. In contrast to the dimeric quaternary structure of most MDHs, these MDHs are tetramers and are structurally related to tetrameric malate dehydrogenases from Archaea and to lactate dehydrogenases. The tetramers are dimers of dimers, where the structures of each subunit and the dimers are similar to the dimeric malate dehydrogenases. The difference in optimal growth temperature of the corresponding organisms is relatively small, ranging from 32 to 55 degrees C. Nevertheless, on the basis of the four crystal structures, a number of factors that are likely to contribute to the relative thermostability in the present series have been identified. It appears from the results obtained, that the difference in thermostability between MDH from the mesophilic Chlorobium vibrioforme on one hand and from the moderate thermophile Chlorobium tepidum on the other hand is mainly due to the presence of polar residues that form additional hydrogen bonds within each subunit. Furthermore, for the even more thermostable Chloroflexus aurantiacus MDH, the use of charged residues to form additional ionic interactions across the dimer-dimer interface is favored. This enzyme has a favorable intercalation of His-Trp as well as additional aromatic contacts at the monomer-monomer interface in each dimer. A structural alignment of tetrameric and dimeric prokaryotic MDHs reveal that structural elements that differ among dimeric and tetrameric MDHs are located in a few loop regions.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Ribbon diagram of the full MDH tetramer with close-up views of two regions in ca-MDH and cv-MDH containing residues that interact across the dimer-dimer interface. The upper panel shows polar interactions across the 2-fold P-axis (A-C) while the lower panel illustrates differences in ionic interactions. The Glu23 (in ca-MDH only) and Asp55 form contacts to residues 241 and 243 between monomers related by the 2-fold R-axis (A-D). Glu164 (in ca-MDH only) and Asp165 interact with residues across the P-axis (B-D). All these interactions occur also on symmetry-related interfaces.
Figure 6.
Figure 6. Arg18-Glu/Asp21 interactions. Ball-and-stick representation of the hydrogen bond interactions between Arg18 and Glu/Asp21 in ct-MDH, hybrid-MDH and cv-MDH, which is probably the major interaction that governs differences in thermostability between the closely related hybrid and cv-MDH. The hydrogen bond distances are mean distances for each interaction.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 707-721) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19250316 E.Lundberg, A.Olofsson, G.T.Westermark, and A.E.Sauer-Eriksson (2009).
Stability and fibril formation properties of human and fish transthyretin, and of the Escherichia coli transthyretin-related protein.
  FEBS J, 276, 1999-2011.  
18397532 S.Paul, S.K.Bag, S.Das, E.T.Harvill, and C.Dutta (2008).
Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes.
  Genome Biol, 9, R70.  
17683333 M.Tehei, and G.Zaccai (2007).
Adaptation to high temperatures through macromolecular dynamics by neutron scattering.
  FEBS J, 274, 4034-4043.  
17401542 R.Stokke, M.Karlström, N.Yang, I.Leiros, R.Ladenstein, N.K.Birkeland, and I.H.Steen (2007).
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.
  Extremophiles, 11, 481-493.
PDB code: 2iv0
  18007057 T.Fujii, T.Oikawa, I.Muraoka, K.Soda, and Y.Hata (2007).
Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 983-986.  
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.  
16547052 S.Friedmann, A.Steindorf, B.E.Alber, and G.Fuchs (2006).
Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus.
  J Bacteriol, 188, 2646-2655.  
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.  
16237006 L.Gakhar, Z.A.Malik, C.C.Allen, D.A.Lipscomb, M.J.Larkin, and S.Ramaswamy (2005).
Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase.
  J Bacteriol, 187, 7222-7231.
PDB codes: 2b1x 2b24
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.  
15532068 C.H.Chan, H.K.Liang, N.W.Hsiao, M.T.Ko, P.C.Lyu, and J.K.Hwang (2004).
Relationship between local structural entropy and protein thermostability.
  Proteins, 57, 684-691.  
15252706 D.Seo, K.Kamino, K.Inoue, and H.Sakurai (2004).
Purification and characterization of ferredoxin-NADP+ reductase encoded by Bacillus subtilis yumC.
  Arch Microbiol, 182, 80-89.  
12596260 E.Bismuto, F.Febbraio, S.Limongelli, R.Briante, and R.Nucci (2003).
Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability.
  Proteins, 51, 10-20.  
12943843 J.K.Yano, and T.L.Poulos (2003).
New understandings of thermostable and peizostable enzymes.
  Curr Opin Biotechnol, 14, 360-365.  
12843403 J.L.England, B.E.Shakhnovich, and E.I.Shakhnovich (2003).
Natural selection of more designable folds: a mechanism for thermophilic adaptation.
  Proc Natl Acad Sci U S A, 100, 8727-8731.  
12902281 Y.W.Kim, J.H.Choi, J.W.Kim, C.Park, J.W.Kim, H.Cha, S.B.Lee, B.H.Oh, T.W.Moon, and K.H.Park (2003).
Directed evolution of Thermus maltogenic amylase toward enhanced thermal resistance.
  Appl Environ Microbiol, 69, 4866-4874.  
12323355 B.van den Burg, and V.G.Eijsink (2002).
Selection of mutations for increased protein stability.
  Curr Opin Biotechnol, 13, 333-337.  
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.