6DHK

Bovine glutamate dehydrogenase complexed with ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation.

Banerjee, S., Schmidt, T., Fang, J., Stanley, C.A., Smith, T.J.

(2003) Biochemistry 42: 3446-3456

  • DOI: 10.1021/bi0206917
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Unlike GDH from bacteria, mammalian GDH exhibits negative cooperativity with respect to coenzyme, activation ...

    Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Unlike GDH from bacteria, mammalian GDH exhibits negative cooperativity with respect to coenzyme, activation by ADP, and inhibition by GTP. Presented here are the structures of apo bovine GDH, bovine GDH complexed with ADP, and the R463A mutant form of human GDH (huGDH) that is insensitive to ADP activation. In the absence of active site ligands, the catalytic cleft is in the open conformation, and the hexamers form long polymers in the crystal cell with more interactions than found in the abortive complex crystals. This is consistent with the fact that ADP promotes aggregation in solution. ADP is shown to bind to the second, inhibitory, NADH site yet causes activation. The beta-phosphates of the bound ADP interact with R459 (R463 in huGDH) on the pivot helix. The structure of the ADP-resistant, R463A mutant of human GDH is identical to native GDH with the exception of the truncated side chain on the pivot helix. Together, these results strongly suggest that ADP activates by facilitating the opening of the catalytic cleft. From alignment of GDH from various sources, it is likely that the antenna evolved in the protista prior to the formation of purine regulatory sites. This suggests that there was some selective advantage of the antenna itself and that animals evolved new functions for GDH through the addition of allosteric regulation.

    Organizational Affiliation: 

    Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate dehydrogenase 1, mitochondrial
A, B, C, D, E, F, G, H, I, J, K, L
496Bos taurusMutation(s): 0 
Gene Names: GLUD1 (GLUD)
EC: 1.4.1.3
Find proteins for P00366 (Bos taurus)
Go to Gene View: GLUD1
Go to UniProtKB:  P00366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download SDF File 
Download CCD File 
A, B, C, D, F, G, H, I, J, K, L
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.382α = 90.00
b = 172.160β = 90.00
c = 439.904γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2018-05-20 
  • Released Date: 2018-07-25 
  • Deposition Author(s): Smith, T.J.

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release