1HWY

BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.

Smith, T.J.Peterson, P.E.Schmidt, T.Fang, J.Stanley, C.A.

(2001) J.Mol.Biol. 307: 707-720

  • DOI: 10.1006/jmbi.2001.4499
  • Primary Citation of Related Structures:  1HWZ
  • Also Cited By: 3MW9

  • PubMed Abstract: 
  • Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric ...

    Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules. The major allosteric inhibitors are GTP and NADH and the two main allosteric activators are ADP and NAD(+). The structures presented here have refined and modified the previous structural model of allosteric regulation inferred from the original boGDH.NADH.GLU.GTP complex. The boGDH.NAD(+).alpha-KG complex structure clearly demonstrates that the second coenzyme-binding site lies directly under the "pivot helix" of the NAD(+) binding domain. In this complex, phosphates are observed to occupy the inhibitory GTP site and may be responsible for the previously observed structural stabilization by polyanions. The boGDH.NADPH.GLU.GTP complex shows the location of the additional phosphate on the active site coenzyme molecule and the GTP molecule bound to the GTP inhibitory site. As expected, since NADPH does not bind well to the second coenzyme site, no evidence of a bound molecule is observed at the second coenzyme site under the pivot helix. Therefore, these results suggest that the inhibitory GTP site is as previously identified. However, ADP, NAD(+), and NADH all bind under the pivot helix, but a second GTP molecule does not. Kinetic analysis of a hyperinsulinism/hyperammonemia mutant strongly suggests that ATP can inhibit the reaction by binding to the GTP site. Finally, the fact that NADH, NAD(+), and ADP all bind to the same site requires a re-analysis of the previous models for NADH inhibition.


    Related Citations: 
    • The Structure of Bovine Glutamate Dehydrogenase Provides Insights Into the Mechanism of Allostery
      Peterson, P.E.,Smith, T.J.
      (1999) Structure 7: 769
    • Crystallization and Characterization of Bovine Liver Glutamate Dehydrogenase
      Peterson, P.E.,Pierce, J.,Smith, T.J.
      (1997) J.Struct.Biol. 120: 73


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. tom@bragg.bio.purdue.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE DEHYDROGENASE
A, B, C, D, E, F
501Bos taurusGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 122.500α = 90.00
b = 101.000β = 102.20
c = 164.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance