4BHT

Structural Determinants of Cofactor Specificity and Domain Flexibility in Bacterial Glutamate Dehydrogenases

Replaces:  2YFG

Summary for 4BHT

• Entry DOI: 10.2210/pdb4bht/pdb
• Descriptor: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE, GLYCEROL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (5 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 6
• Total formula weight: 293901.51

Authors

Oliveira, T.,Sharkey, M.,Engel, P.,Khan, A. (deposition date: 2013-04-06, release date: 2013-06-19, Last modification date: 2023-12-20)

Primary citation

Sharkey, M.A.,Oliveira, T.F.,Engel, P.C.,Khan, A.R.
Structure of Nadp(+) -Dependent Glutamate Dehydrogenase from Escherichia Coli: Reflections on the Basis of Coenzyme Specificity in the Family of Glutamate Dehydrogenases.
FEBS J., 280:4681-, 2013

PubMed Abstract: Glutamate dehydrogenases (GDHs; EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate, using NAD(+) and/or NADP(+) as a cofactor. Subunits of homo-hexameric bacterial enzymes comprise a substrate-binding domain I followed by a nucleotide-binding domain II. The reaction occurs in a catalytic cleft between the two domains. Although conserved residues in the nucleotide-binding domains of various dehydrogenases have been linked to cofactor preferences, the structural basis for specificity in the GDH family remains poorly understood. Here, the refined crystal structure of Escherichia coli GDH in the absence of reactants is described at 2.5-Å resolution. Modelling of NADP(+) in domain II reveals the potential contribution of positively charged residues from a neighbouring α-helical hairpin to phosphate recognition. In addition, a serine that follows the P7 aspartate is presumed to form a hydrogen bond with the 2'-phosphate. Mutagenesis and kinetic analysis confirms the importance of these residues in NADP(+) recognition. Surprisingly, one of the positively charged residues is conserved in all sequences of NAD(+)-dependent enzymes, but the conformations adopted by the corresponding regions in proteins whose structure has been solved preclude their contribution to the coordination of the 2'-ribose phosphate of NADP(+). These studies clarify the sequence-structure relationships in bacterial GDHs, revealing that identical residues may specify different coenzyme preferences, depending on the structural context. Primary sequence alone is therefore not a reliable guide for predicting coenzyme specificity. We also consider how it is possible for a single sequence to accommodate both coenzymes in the dual-specificity GDHs of animals.

PubMed: 23879525
DOI: 10.1111/FEBS.12439

Experimental method

X-RAY DIFFRACTION (2.5 Å)