Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Work: 0.173 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1006/jmbi.1993.1665
  • Primary Citation of Related Structures:  

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMATE DEHYDROGENASE449[Clostridium] symbiosumMutation(s): 0 
Find proteins for P24295 (Clostridium symbiosum)
Explore P24295 
Go to UniProtKB:  P24295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24295
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLU

Download Ideal Coordinates CCD File 
C5 H9 N O4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Work: 0.173 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.8α = 90
b = 162.8β = 90
c = 102.8γ = 120
Software Package:
Software NamePurpose
PHASEmodel building
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description