1L1F

Structure of human glutamate dehydrogenase-apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of apo human glutamate dehydrogenase details subunit communication and allostery.

Smith, T.J.Schmidt, T.Fang, J.Wu, J.Siuzdak, G.Stanley, C.A.

(2002) J.Mol.Biol. 318: 765-777

  • DOI: 10.1016/S0022-2836(02)00161-4

  • PubMed Abstract: 
  • The structure of human glutamate dehydrogenase (GDH) has been determined in the absence of active site and regulatory ligands. Compared to the structures of bovine GDH that were complexed with coenzyme and substrate, the NAD binding domain is rotated ...

    The structure of human glutamate dehydrogenase (GDH) has been determined in the absence of active site and regulatory ligands. Compared to the structures of bovine GDH that were complexed with coenzyme and substrate, the NAD binding domain is rotated away from the glutamate-binding domain. The electron density of this domain is more disordered the further it is from the pivot helix. Mass spectrometry results suggest that this is likely due to the apo form being more dynamic than the closed form. The antenna undergoes significant conformational changes as the catalytic cleft opens. The ascending helix in the antenna moves in a clockwise manner and the helix in the descending strand contracts in a manner akin to the relaxation of an extended spring. A number of spontaneous mutations in this antenna region cause the hyperinsulinism/hyperammonemia syndrome by decreasing GDH sensitivity to the inhibitor, GTP. Since these residues do not directly contact the bound GTP, the conformational changes in the antenna are apparently crucial to GTP inhibition. In the open conformation, the GTP binding site is distorted such that it can no longer bind GTP. In contrast, ADP binding benefits by the opening of the catalytic cleft since R463 on the pivot helix is pushed into contact distance with the beta-phosphate of ADP. These results support the previous proposal that purines regulate GDH activity by altering the dynamics of the NAD binding domain. Finally, a possible structural mechanism for negative cooperativity is presented.


    Organizational Affiliation

    Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA. tsmith@danforthcenter.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate Dehydrogenase 1
A, B, C, D, E, F
505Homo sapiensMutation(s): 0 
Gene Names: GLUD1 (GLUD)
EC: 1.4.1.3
Find proteins for P00367 (Homo sapiens)
Go to Gene View: GLUD1
Go to UniProtKB:  P00367
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.262 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 97.800α = 86.26
b = 98.800β = 70.28
c = 124.200γ = 60.34
Software Package:
Software NamePurpose
Omodel building
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance