PDBsum entry 1aup

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protein links
Oxidoreductase PDB id
Protein chain
427 a.a. *
Waters ×40
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Glutamate dehydrogenase
Structure: NAD-specific glutamate dehydrogenase. Chain: a. Engineered: yes. Mutation: yes
Source: Clostridium symbiosum. Organism_taxid: 1512. Gene: gdh. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Hexamer (from PDB file)
2.50Å     R-factor:   0.190    
Authors: P.J.Baker,M.L.Waugh,T.J.Stillman,A.P.Turnbull,D.W.Rice
Key ref:
P.J.Baker et al. (1997). Determinants of substrate specificity in the superfamily of amino acid dehydrogenases. Biochemistry, 36, 16109-16115. PubMed id: 9405044 DOI: 10.1021/bi972024x
01-Sep-97     Release date:   18-Mar-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P24295  (DHE2_CLOSY) -  NAD-specific glutamate dehydrogenase
450 a.a.
427 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Glutamate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH
+ H(2)O
+ NAD(+)
= 2-oxoglutarate
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  


DOI no: 10.1021/bi972024x Biochemistry 36:16109-16115 (1997)
PubMed id: 9405044  
Determinants of substrate specificity in the superfamily of amino acid dehydrogenases.
P.J.Baker, M.L.Waugh, X.G.Wang, T.J.Stillman, A.P.Turnbull, P.C.Engel, D.W.Rice.
The subunit of the enzyme glutamate dehydrogenase comprises two domains separated by a cleft harboring the active site. One domain is responsible for dinucleotide binding and the other carries the majority of residues which bind the substrate. During the catalytic cycle a large movement between the two domains occurs, closing the cleft and bringing the C4 of the nicotinamide ring and the Calpha of the substrate into the correct positioning for hydride transfer. In the active site, two residues, K89 and S380, make interactions with the gamma-carboxyl group of the glutamate substrate. In leucine dehydrogenase, an enzyme belonging to the same superfamily, the equivalent residues are L40 and V294, which create a more hydrophobic specificity pocket and provide an explanation for their differential substrate specificity. In an attempt to change the substrate specificity of glutamate dehydrogenase toward that of leucine dehydrogenase, a double mutant, K89L,S380V, of glutamate dehydrogenase has been constructed. Far from having a high specificity for leucine, this mutant appears to be devoid of any catalytic activity over a wide range of substrates tested. Determination of the three-dimensional structure of the mutant enzyme has shown that the loss of function is related to a disordering of residues linking the enzyme's two domains, probably arising from a steric clash between the valine side chain, introduced at position 380 in the mutant, and a conserved threonine residue, T193. In leucine dehydrogenase the steric clash between the equivalent valine and threonine side chains (V294, T134) does not occur owing to shifts of the main chain to which these side chains are attached. Thus, the differential substrate specificity seen in the amino acid dehydrogenase superfamily arises from both the introduction of simple point mutations and the fine tuning of the active site pocket defined by small but significant main chain rearrangements.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20960531 G.Zanotti, and L.Cendron (2010).
Functional and structural aspects of Helicobacter pylori acidic stress response factors.
  IUBMB Life, 62, 715-723.  
19730672 J.Baussand, and A.Carbone (2009).
A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence.
  PLoS Comput Biol, 5, e1000488.  
18491387 S.M.Tripathi, and R.Ramachandran (2008).
Crystal structures of the Mycobacterium tuberculosis secretory antigen alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures "open" and "closed" enzyme conformations.
  Proteins, 72, 1089-1095.
PDB codes: 2voe 2voj
15634349 B.M.Martins, S.Macedo-Ribeiro, J.Bresser, W.Buckel, and A.Messerschmidt (2005).
Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans.
  FEBS J, 272, 269-281.
PDB code: 1xdw
12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
  Structure, 10, 1435-1451.  
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
11722565 X.G.Wang, K.L.Britton, T.J.Stillman, D.W.Rice, and P.C.Engel (2001).
Conversion of a glutamate dehydrogenase into methionine/norleucine dehydrogenase by site-directed mutagenesis.
  Eur J Biochem, 268, 5791-5799.  
10508675 A.E.Todd, C.A.Orengo, and J.M.Thornton (1999).
Evolution of protein function, from a structural perspective.
  Curr Opin Chem Biol, 3, 548-556.  
10099128 P.J.O'Brien, and D.Herschlag (1999).
Catalytic promiscuity and the evolution of new enzymatic activities.
  Chem Biol, 6, R91.  
10512837 R.M.Daniel, J.L.Finney, V.Réat, R.Dunn, M.Ferrand, and J.C.Smith (1999).
Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution.
  Biophys J, 77, 2184-2190.  
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