2YFH

Structure of a Chimeric Glutamate Dehydrogenase


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASEABCDEF448[Clostridium] symbiosumEscherichia coliMutation(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
Protein Feature View
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  • Reference Sequence
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 = 100.102α = 116.54
b = 113.859β = 101.54
c = 109.581γ = 104.09
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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