1BGV

GLUTAMATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1131-1139

  • DOI: 10.1006/jmbi.1993.1665

  • PubMed Abstract: 
  • We have solved the structure of the binary complex of the glutamate dehydrogenase from Clostridium symbiosum with glutamate to 1.9 A resolution. In this complex, the glutamate side-chain lies in a pocket on the enzyme surface and a key determinant of ...

    We have solved the structure of the binary complex of the glutamate dehydrogenase from Clostridium symbiosum with glutamate to 1.9 A resolution. In this complex, the glutamate side-chain lies in a pocket on the enzyme surface and a key determinant of the enzymic specificity is an interaction of the substrate gamma-carboxyl group with the amino group of Lys89. In the apo-enzyme, Lys113 from the catalytic domain forms an important hydrogen bond to Asn373, in the NAD(+)-binding domain. On glutamate binding, the side-chain of this lysine undergoes a significant movement in order to optimize its hydrogen bonding to the alpha-carboxyl group of the substrate. Despite this shift, the interaction between Lys113 and Asn373 is maintained by a large-scale conformational change that closes the cleft between the two domains. Modelling studies indicate that in this "closed" conformation the C-4 of the nicotinamide ring and the alpha-carbon atom of the amino acid substrate are poised for efficient hydride transfer. Examination of the structure has led to a proposal for the catalytic activity of the enzyme, which involves Asp165 as a general base, and an enzyme-bound water molecule, hydrogen-bonded to an uncharged lysine residue, Lys125, as an attacking nucleophile in the reaction.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE DEHYDROGENASE
A
449Clostridium symbiosumGene Names: gdh
EC: 1.4.1.2
Find proteins for P24295 (Clostridium symbiosum)
Go to UniProtKB:  P24295
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.173 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 162.800α = 90.00
b = 162.800β = 90.00
c = 102.800γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement
PHASEmodel building
MOSFLMdata reduction
ROTAVATA)data scaling
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance