Bovine glutamate dehydrogenase in ternary complex with the allosteric activators ADP and leucine

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase.

Aleshin, V.A.Bunik, V.I.Bruch, E.M.Bellinzoni, M.

(2022) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms231911306
  • Primary Citation of Related Structures:  
    8AR7, 8AR8

  • PubMed Abstract: 

    Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here, we aim at deciphering a structural basis for the GDH allosteric activation using bovine GDH as a model. For the first time, we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion, resolved to 2.45 Å. An improved 2.4-angstrom resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.

  • Organizational Affiliation

    Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase (NAD(P)(+))
A, B, C, D, E
A, B, C, D, E, F
561Bos taurusMutation(s): 0 
Find proteins for A0A140T871 (Bos taurus)
Explore A0A140T871 
Go to UniProtKB:  A0A140T871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140T871
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
N [auth C]
R [auth D]
U [auth E]
G [auth A],
K [auth B],
N [auth C],
R [auth D],
U [auth E],
W [auth F]
C10 H15 N5 O10 P2
LEU (Subject of Investigation/LOI)
Query on LEU

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
M [auth B]
P [auth C]
Q [auth D]
I [auth A],
J [auth A],
M [auth B],
P [auth C],
Q [auth D],
T [auth E]
C6 H13 N O2
Query on K

Download Ideal Coordinates CCD File 
H [auth A]
L [auth B]
O [auth C]
S [auth D]
V [auth E]
H [auth A],
L [auth B],
O [auth C],
S [auth D],
V [auth E],
X [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.877α = 90
b = 178.705β = 104
c = 123.884γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Pasteur InstituteFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description