2YFH

Structure of a Chimeric Glutamate Dehydrogenase

Summary for 2YFH

• Entry DOI: 10.2210/pdb2yfh/pdb
• Related: 2YFG
• Descriptor: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE (2 entities in total)
• Functional Keywords: oxidoreductase, chimera
• Biological source: CLOSTRIDIUM SYMBIOSUM; More
• Total number of polymer chains: 6
• Total formula weight: 290578.73

Authors

Oliveira, T.,Panjikar, S.,Sharkey, M.A.,Carrigan, J.B.,Hamza, M.,Engel, P.C.,Khan, A.R. (deposition date: 2011-04-05, release date: 2012-04-04, Last modification date: 2023-12-20)

Primary citation

Oliveira, T.,Sharkey, M.A.,Engel, P.C.,Khan, A.R.
Crystal Structure of a Chimaeric Bacterial Glutamate Dehydrogenase.
Acta Crystallogr.,Sect.F, 72:462-, 2016

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.

PubMed: 27303899
DOI: 10.1107/S2053230X16007305

Experimental method

X-RAY DIFFRACTION (2.695 Å)