Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 280.68 kDa 
• Atom Count: 19628 
• Modelled Residue Count: 2433 
• Deposited Residue Count: 2544 
• Unique protein chains: 1

3K92

Crystal structure of a E93K mutant of the majour Bacillus subtilis glutamate dehydrogenase RocG

• PDB DOI: 10.2210/pdb3K92/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-10-15 Released: 2010-06-02 
• Deposition Author(s): Gunka, K., Newman, J.A., Commichau, F.M., Herzberg, C., Rodrigues, C., Hewitt, L., Lewis, R.J., Stulke, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties

Gunka, K., Newman, J.A., Commichau, F.M., Herzberg, C., Rodrigues, C., Hewitt, L., Lewis, R.J., Stulke, J.

(2010) J Mol Biol 400: 815-827

• PubMed: 20630473 
• DOI: 10.1016/j.jmb.2010.05.055
• Primary Citation of Related Structures:  
  3K8Z, 3K92


• PubMed Abstract: 
  

Any signal transduction requires communication between a sensory component and an effector. Some enzymes engage in signal perception and transduction, as well as in catalysis, and these proteins are known as "trigger" enzymes. In this report, we detail the trigger properties of RocG, the glutamate dehydrogenase of Bacillus subtilis. RocG not only deaminates the key metabolite glutamate to form alpha-ketoglutarate but also interacts directly with GltC, a LysR-type transcription factor that regulates glutamate biosynthesis from alpha-ketoglutarate, thus linking the two metabolic pathways. We have isolated mutants of RocG that separate the two functions. Several mutations resulted in permanent inactivation of GltC as long as a source of glutamate was present. These RocG proteins have lost their ability to catabolize glutamate due to a strongly reduced affinity for glutamate. The second class of mutants is exemplified by the replacement of aspartate residue 122 by asparagine. This mutant protein has retained enzymatic activity but has lost the ability to control the activity of GltC. Crystal structures of glutamate dehydrogenases that permit a molecular explanation of the properties of the various mutants are presented. Specifically, we may propose that D122N replacement affects the surface of RocG. Our data provide evidence for a correlation between the enzymatic activity of RocG and its ability to inactivate GltC, and thus give insights into the mechanism that couples the enzymatic activity of a trigger enzyme to its regulatory function.

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Organizational Affiliation: 

Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-specific glutamate dehydrogenase	A, B, C, D, E, F	424	Bacillus subtilis	Mutation(s): 1  EC: 1.4.1.2
UniProt
Find proteins for P39633 (Bacillus subtilis (strain 168)) Explore P39633  Go to UniProtKB:  P39633

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A], H [auth C], I [auth D], J [auth E], K [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.614	α = 90
b = 143.072	β = 90
c = 162.607	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-15 
• Released Date: 2010-06-02 
Deposition Author(s): Gunka, K., Newman, J.A., Commichau, F.M., Herzberg, C., Rodrigues, C., Hewitt, L., Lewis, R.J., Stulke, J.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-22
  Changes: Database references