Crystal structure of Glutamate dehydrogenase from Peptoniphilus asaccharolyticus

Experimental Data Snapshot

  • Resolution: 2.94 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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Crystal Structure of Nad-Dependent Peptoniphilus Asaccharolyticus Glutamate Dehydrogenase Reveals Determinants of Cofactor Specificity.

Oliveira, T.Panjikar, S.Carrigan, J.B.Hamza, M.Engel, P.C.Khan, A.R.

(2012) J Struct Biol 177: 543

  • DOI: https://doi.org/10.1016/j.jsb.2011.10.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Glutamate dehydrogenases (EC catalyse the oxidative deamination of l-glutamate to α-ketoglutarate using NAD(P) as a cofactor. The bacterial enzymes are hexamers and each polypeptide consists of an N-terminal substrate-binding (Domain I) followed by a C-terminal cofactor-binding segment (Domain II). The reaction takes place at the junction of the two domains, which move as rigid bodies and are presumed to narrow the cleft during catalysis. Distinct signature sequences in the nucleotide-binding domain have been linked to NAD(+) vs. NADP(+) specificity, but they are not unambiguous predictors of cofactor preferences. Here, we have determined the crystal structure of NAD(+)-specific Peptoniphilus asaccharolyticus glutamate dehydrogenase in the apo state. The poor quality of native crystals was resolved by derivatization with selenomethionine, and the structure was solved by single-wavelength anomalous diffraction methods. The structure reveals an open catalytic cleft in the absence of substrate and cofactor. Modeling of NAD(+) in Domain II suggests that a hydrophobic pocket and polar residues contribute to nucleotide specificity. Mutagenesis and isothermal titration calorimetry studies of a critical glutamate at the P7 position of the core fingerprint confirms its role in NAD(+) binding. Finally, the cofactor binding site is compared with bacterial and mammalian enzymes to understand how the amino acid sequences and three-dimensional structures may distinguish between NAD(+) vs. NADP(+) recognition.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
421Peptoniphilus asaccharolyticusMutation(s): 0 
Find proteins for P28997 (Peptoniphilus asaccharolyticus)
Explore P28997 
Go to UniProtKB:  P28997
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28997
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.94 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.314α = 90
b = 153.314β = 90
c = 318.993γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Other