5IJZ

Crystal structure of glutamate dehydrogenase(GDH) from Corynebacterium glutamicum

Summary for 5IJZ

• Entry DOI: 10.2210/pdb5ijz/pdb
• Descriptor: NADP-specific glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 2-OXOGLUTARIC ACID, ... (4 entities in total)
• Functional Keywords: glutamate dehydrogenase, oxidoreductase
• Biological source: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
• Total number of polymer chains: 12
• Total formula weight: 596558.75

Authors

Son, H.-F.,Kim, K.-J. (deposition date: 2016-03-03, release date: 2016-03-23, Last modification date: 2023-11-08)

Primary citation

Son, H.-F.,Kim, K.-J.
Structural insights into domain movement and cofactor specificity of glutamate dehydrogenase from Corynebacterium glutamicum
BIOCHEM.BIOPHYS.RES.COMMUN., 459:387-392, 2015

PubMed Abstract: Glutamate dehydrogenase (GDH) is an enzyme involved in the synthesis of amino acids by converting glutamate to α-ketoglutarate, and vice versa. To investigate the molecular mechanism of GDH, we determined a crystal structure of the Corynebacterium glutamicum-derived GDH (CgGDH) in complex with its NADP cofactor and α-ketoglutarate substrate. CgGDH functions as a hexamer, and each CgGDH monomer comprises 2 separate domains; a Rossmann fold cofactor-binding domain and a substrate-binding domain. The structural comparison between the apo- and cofactor/substrate-binding forms revealed that the CgGDH enzyme undergoes a domain movement during catalysis. In the apo-form, CgGDH exists as an open state, and upon binding of the substrate and cofactor the protein undergoes a conformation change to a closed state. Our structural study also revealed that CgGDH has cofactor specificity for NADP, but not NAD, and this was confirmed by GDH activity measurements. Residues involved in the stabilization of the NADP cofactor and the α-ketoglutarate substrate were identified, and their roles in substrate/cofactor binding were confirmed by site-directed mutagenesis experiments.

PubMed: 25727019
DOI: 10.1016/j.bbrc.2015.02.109

Experimental method

X-RAY DIFFRACTION (2.29 Å)