3MVO

Crystal structure of bovine glutamate dehydrogenase complexed with Eu3+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis.

Bailey, J.Powell, L.Sinanan, L.Neal, J.Li, M.Smith, T.Bell, E.

(2011) Febs J. 278: 3140-3151

  • DOI: 10.1111/j.1742-4658.2011.08240.x
  • Primary Citation of Related Structures:  3MVQ

  • PubMed Abstract: 
  • Bovine glutamate dehydrogenase is potently inhibited by zinc and the major impact is on V(max) suggesting a V-type effect on catalysis or product release. Zinc inhibition decreases as glutamate concentrations decrease suggesting a role for subunit in ...

    Bovine glutamate dehydrogenase is potently inhibited by zinc and the major impact is on V(max) suggesting a V-type effect on catalysis or product release. Zinc inhibition decreases as glutamate concentrations decrease suggesting a role for subunit interactions. With the monocarboxylic amino acid norvaline, which gives no evidence of subunit interactions, zinc does not inhibit. Zinc significantly decreases the size of the pre-steady state burst in the reaction but does not affect NADPH binding in the enzyme-NADPH-glutamate complex that governs the steady state turnover, again suggesting that zinc disrupts subunit interactions required for catalytic competence. While differential scanning calorimetry suggests zinc binds and induces a slightly conformationally more rigid state of the protein, limited proteolysis indicates that regions in the vicinity of the antennae regions and the trimer-trimer interface become more flexible. The structures of glutamate dehydrogenase bound with zinc and europium show that zinc binds between the three dimers of subunits in the hexamer, a region shown to bind novel inhibitors that block catalytic turnover, which is consistent with the above findings. In contrast, europium binds to the base of the antenna region and appears to abrogate the inhibitory effect of zinc. Structures of various states of the enzyme have shown that both regions are heavily involved in the conformational changes associated with catalytic turnover. These results suggest that the V-type inhibition produced with glutamate as the substrate results from disruption of subunit interactions necessary for efficient catalysis rather than by a direct effect on the active site conformation.


    Organizational Affiliation

    Gustavus Adolphus College, St Peter, MN, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate dehydrogenase 1, mitochondrial
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
GLU
Query on GLU

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
EU3
Query on EU3

Download SDF File 
Download CCD File 
A, D
EUROPIUM (III) ION
Eu
LNBHUCHAFZUEGJ-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 121.110α = 90.00
b = 98.760β = 101.55
c = 165.640γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHENIXrefinement
PROTEUM PLUSdata reduction
CNSphasing
CNSrefinement
PROTEUM PLUSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-05-04 
  • Released Date: 2011-05-04 
  • Deposition Author(s): Smith, T.J., Li, M.

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-31
    Type: Database references