Biological Assembly 1  

 3D View: Structure | Electron Density

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: 290.58 kDa 
• Atom Count: 20640 
• Residue Count: 2677 
• Unique protein chains: 1

2YFH

Structure of a Chimeric Glutamate Dehydrogenase

• DOI: 10.2210/pdb2YFH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): [Clostridium] symbiosum, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-05 Released: 2012-04-04 
• Deposition Author(s): Oliveira, T., Panjikar, S., Sharkey, M.A., Carrigan, J.B., Hamza, M., Engel, P.C., Khan, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.282 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Literature

Crystal Structure of a Chimaeric Bacterial Glutamate Dehydrogenase.

Oliveira, T., Sharkey, M.A., Engel, P.C., Khan, A.R.

(2016) Acta Crystallogr F Struct Biol Commun 72: 462

• PubMed: 27303899 
• DOI: 10.1107/S2053230X16007305
• Primary Citation of Related Structures:  
  2YFH


• PubMed Abstract: 
  

Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P)(+) as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD(+) versus NADP(+), but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies, as shown by the apo structure of glutamate dehydrogenase from Clostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia coli enzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP(+) cofactor from the parent E. coli domain II, although there are subtle differences in catalytic activity.

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Organizational Affiliation: 

School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE	A, B, C, D, E, F	448	[Clostridium] symbiosum, Escherichia coli	Mutation(s): 0  EC: 1.4.1.4 (PDB Primary Data), 1.4.1.3 (PDB Primary Data), 1.4.1.2 (PDB Primary Data)
Find proteins for P00370 (Escherichia coli (strain K12)) Explore P00370  Go to UniProtKB:  P00370
Find proteins for E7GGS1 ([Clostridium] symbiosum WAL-14163) Explore E7GGS1  Go to UniProtKB:  E7GGS1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.282 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.102	α = 116.54
b = 113.859	β = 101.54
c = 109.581	γ = 104.09

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-05 
• Released Date: 2012-04-04 
Deposition Author(s): Oliveira, T., Panjikar, S., Sharkey, M.A., Carrigan, J.B., Hamza, M., Engel, P.C., Khan, A.R.

Revision History 

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2016-06-29
  Changes: Database references
• Version 1.3: 2017-03-15
  Changes: Source and taxonomy