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PDBsum entry 1bvu

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
1bvu
Jmol
Contents
Protein chains
(+ 0 more) 416 a.a. *
* Residue conservation analysis
PDB id:
1bvu
Name: Oxidoreductase
Title: Glutamate dehydrogenase from thermococcus litoralis
Structure: Protein (glutamate dehydrogenase). Chain: a, b, c, d, e, f. Ec: 1.4.1.3
Source: Thermococcus litoralis. Organism_taxid: 2265
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.192     R-free:   0.308
Authors: P.J.Baker,K.L.Britton,K.S.Yip,T.J.Stillman,D.W.Rice
Key ref:
K.L.Britton et al. (1999). Structure determination of the glutamate dehydrogenase from the hyperthermophile Thermococcus litoralis and its comparison with that from Pyrococcus furiosus. J Mol Biol, 293, 1121-1132. PubMed id: 10547290 DOI: 10.1006/jmbi.1999.3205
Date:
20-Jul-99     Release date:   18-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q56304  (DHE3_THELI) -  Glutamate dehydrogenase
Seq:
Struc:
419 a.a.
416 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.4.1.3  - Glutamate dehydrogenase (NAD(P)(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate + H2O + NAD(P)(+) = 2-oxoglutarate + NH3 + NAD(P)H
L-glutamate
+ H(2)O
+ NAD(P)(+)
= 2-oxoglutarate
+ NH(3)
+ NAD(P)H
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   2 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.3205 J Mol Biol 293:1121-1132 (1999)
PubMed id: 10547290  
 
 
Structure determination of the glutamate dehydrogenase from the hyperthermophile Thermococcus litoralis and its comparison with that from Pyrococcus furiosus.
K.L.Britton, K.S.Yip, S.E.Sedelnikova, T.J.Stillman, M.W.Adams, K.Ma, D.L.Maeder, F.T.Robb, N.Tolliday, C.Vetriani, D.W.Rice, P.J.Baker.
 
  ABSTRACT  
 
Glutamate dehydrogenase catalyses the oxidative deamination of glutamate to 2-oxoglutarate with concomitant reduction of NAD(P)(+), and has been shown to be widely distributed in nature across species ranging from psychrophiles to hyperthermophiles. Extensive characterisation of this enzyme isolated from hyperthermophilic organisms has led to its adoption as a model system for analysing the determinants of thermal stability. The crystal structure of the extremely thermostable glutamate dehydrogenase from Thermococcus litoralis has been determined at 2.5 A resolution, and has been compared to that from the hyperthermophile Pyrococcus furiosus. The two enzymes are 87 % identical in sequence, yet differ 16-fold in their half-lives at 104 degrees C. This is the first reported comparative analysis of the structures of a multisubunit enzyme from two closely related yet distinct hyperthermophilies. The less stable T. litoralis enzyme has a decreased number of ion pair interactions; modified patterns of hydrogen bonding resulting from isosteric sequence changes; substitutions that decrease packing efficiency; and substitutions which give rise to subtle but distinct shifts in both main-chain and side-chain elements of the structure. This analysis provides a rational basis to test ideas on the factors that confer thermal stability in proteins through a combination of mutagenesis, calorimetry, and structural studies.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo diagrams of a single subunit of Tl GluDH. The organisation of the subunit into two domains, sep- arated by a deep cleft, can be seen. In this view, the 3-fold axis of the GluDH hexamer runs vertically with domain I lying uppermost and domain II in the lower portion of the Figure. (a) Schematic representation with strands (a-m) and helices (1-14) marked. (b) C a trace with every tenth residue indicated by a black dot. The Figure was prepared using MOLSCRIPT (Kraulis, 1991).
Figure 3.
Figure 3. Diagrams of the superposition of the structures of the GluDHs from Pf (red) and Tl (blue) produced using the program MIDASPLUS (Ferrin et al., 1988). Highlighting the local differences in structure between the two enzymes as a result of complementary sequence changes: (a) I198V, L227M and V317L; (b) V204A and Y382W; (c) the isosteric sequence change V322T resulting in the formation of an extra hydrogen bond (green dotted line) in the Tl enzyme relative to the Pf GluDH; (d) the packing change I107V.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 1121-1132) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20534574 O.A.Oyeyemi, K.M.Sours, T.Lee, K.A.Resing, N.G.Ahn, and J.P.Klinman (2010).
Temperature dependence of protein motions in a thermophilic dihydrofolate reductase and its relationship to catalytic efficiency.
  Proc Natl Acad Sci U S A, 107, 10074-10079.  
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
16533850 S.Melchionna, R.Sinibaldi, and G.Briganti (2006).
Explanation of the stability of thermophilic proteins based on unique micromorphology.
  Biophys J, 90, 4204-4212.  
16244435 M.I.Khan, K.Ito, H.Kim, H.Ashida, T.Ishikawa, H.Shibata, and Y.Sawa (2005).
Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis.
  Biosci Biotechnol Biochem, 69, 1861-1870.  
15649900 V.P.Hytönen, J.A.Määttä, T.K.Nyholm, O.Livnah, Y.Eisenberg-Domovich, D.Hyre, H.R.Nordlund, J.Hörhä, E.A.Niskanen, T.Paldanius, T.Kulomaa, E.J.Porkka, P.S.Stayton, O.H.Laitinen, and M.S.Kulomaa (2005).
Design and construction of highly stable, protease-resistant chimeric avidins.
  J Biol Chem, 280, 10228-10233.  
15040324 D.A.Cowen (2004).
The upper temperature of life--where do we draw the line?
  Trends Microbiol, 12, 58-60.  
15039563 M.W.Bhuiya, H.Sakuraba, K.Yoneda, T.Ohshima, T.Imagawa, N.Katunuma, and H.Tsuge (2004).
Crystallization and preliminary X-ray diffraction analysis of the hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum.
  Acta Crystallogr D Biol Crystallogr, 60, 715-717.  
14718652 N.Palackal, Y.Brennan, W.N.Callen, P.Dupree, G.Frey, F.Goubet, G.P.Hazlewood, S.Healey, Y.E.Kang, K.A.Kretz, E.Lee, X.Tan, G.L.Tomlinson, J.Verruto, V.W.Wong, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
An evolutionary route to xylanase process fitness.
  Protein Sci, 13, 494-503.  
15206928 Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, and K.Yutani (2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
  Eur J Biochem, 271, 2624-2635.
PDB code: 1v8z
12473121 G.S.Bell, R.J.Russell, H.Connaris, D.W.Hough, M.J.Danson, and G.L.Taylor (2002).
Stepwise adaptations of citrate synthase to survival at life's extremes. From psychrophile to hyperthermophile.
  Eur J Biochem, 269, 6250-6260.
PDB code: 1o7x
12136148 M.W.Bhuiya, H.Tsuge, H.Sakuraba, K.Yoneda, N.Katunuma, and T.Ohshima (2002).
Crystallization and preliminary X-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1.
  Acta Crystallogr D Biol Crystallogr, 58, 1338-1339.  
11282340 D.C.Demirjian, F.Morís-Varas, and C.S.Cassidy (2001).
Enzymes from extremophiles.
  Curr Opin Chem Biol, 5, 144-151.  
11258921 M.Nakasako, T.Fujisawa, S.Adachi, T.Kudo, and S.Higuchi (2001).
Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering.
  Biochemistry, 40, 3069-3079.
PDB code: 1euz
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.