2YFH

Structure of a Chimeric Glutamate Dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.695 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.215 

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.,Sect.F 72: 462

  • DOI: 10.1107/S2053230X16007305

  • 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.,School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
A, B, C, D, E, F
448Escherichia coli (strain K12)[Clostridium] symbiosum WAL-14163
This entity is chimeric
Mutation(s): 0 
Gene Names: gdhA,
EC: 1.4.1.4
Find proteins for P00370 (Escherichia coli (strain K12))
Go to UniProtKB:  P00370
Find proteins for E7GGS1 ([Clostridium] symbiosum WAL-14163)
Go to UniProtKB:  E7GGS1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.695 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.215 
  • 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
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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