1AUP

GLUTAMATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Determinants of substrate specificity in the superfamily of amino acid dehydrogenases.

Baker, P.J.Waugh, M.L.Wang, X.G.Stillman, T.J.Turnbull, A.P.Engel, P.C.Rice, D.W.

(1997) Biochemistry 36: 16109-16115

  • DOI: 10.1021/bi972024x

  • PubMed Abstract: 
  • 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 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.


    Related Citations: 
    • Conformational Flexibility in Glutamate Dehydrogenase. Role of Water in Substrate Recognition and Catalysis
      Stillman, T.J.,Baker, P.J.,Britton, K.L.,Rice, D.W.
      (1993) J.Mol.Biol. 234: 1131
    • Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase
      Baker, P.J.,Britton, K.L.,Engel, P.C.,Farrants, G.W.,Lilley, K.S.,Rice, D.W.,Stillman, T.J.
      (1992) Proteins 12: 75
    • Crystallization of an Nad+-Dependent Glutamate Dehydrogenase from Clostridium Symbiosum
      Rice, D.W.,Hornby, D.P.,Engel, P.C.
      (1985) J.Mol.Biol. 181: 147
    • Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity
      Baker, P.J.,Britton, K.L.,Rice, D.W.,Rob, A.,Stillman, T.J.
      (1992) J.Mol.Biol. 228: 662
    • Structural Relationship between the Hexameric and Tetrameric Family of Glutamate Dehydrogenases
      Britton, K.L.,Baker, P.J.,Rice, D.W.,Stillman, T.J.
      (1992) Eur.J.Biochem. 209: 851
    • Erratum. Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity
      Baker, P.J.,Britton, K.L.,Rice, D.W.,Rob, A.,Stillman, T.J.
      (1993) J.Mol.Biol. 232: 1012
    • The Structure of Pyrococcus Furiosus Glutamate Dehydrogenase Reveals a Key Role for Ion-Pair Networks in Maintaining Enzyme Stability at Extreme Temperatures
      Yip, K.S.,Stillman, T.J.,Britton, K.L.,Artymiuk, P.J.,Baker, P.J.,Sedelnikova, S.E.,Engel, P.C.,Pasquo, A.,Chiaraluce, R.,Consalvi, V.,Scandurra, R.,Rice, D.W.
      (1995) Structure 3: 1147


    Organizational Affiliation

    The Krebs Institute, Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
A
449Clostridium symbiosumGene Names: gdh
EC: 1.4.1.2
Find proteins for P24295 (Clostridium symbiosum)
Go to UniProtKB:  P24295
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 162.900α = 90.00
b = 162.900β = 90.00
c = 100.700γ = 120.00
Software Package:
Software NamePurpose
TFFCmodel building
ROTAVATA)data scaling
TFFCphasing
MOSFLMdata reduction
TNTrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance