1BGV
GLUTAMATE DEHYDROGENASE
Summary for 1BGV
| Entry DOI | 10.2210/pdb1bgv/pdb |
| Descriptor | GLUTAMATE DEHYDROGENASE, GLUTAMIC ACID (3 entities in total) |
| Functional Keywords | oxidoreductase |
| Biological source | Clostridium symbiosum |
| Total number of polymer chains | 1 |
| Total formula weight | 49362.78 |
| Authors | Stillman, T.J.,Baker, P.J.,Britton, K.L.,Rice, D.W. (deposition date: 1998-06-01, release date: 1998-10-14, Last modification date: 2024-02-07) |
| Primary citation | Stillman, T.J.,Baker, P.J.,Britton, K.L.,Rice, D.W. Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J.Mol.Biol., 234:1131-1139, 1993 Cited by PubMed Abstract: We have solved the structure of the binary complex of the glutamate dehydrogenase from Clostridium symbiosum with glutamate to 1.9 A resolution. In this complex, the glutamate side-chain lies in a pocket on the enzyme surface and a key determinant of the enzymic specificity is an interaction of the substrate gamma-carboxyl group with the amino group of Lys89. In the apo-enzyme, Lys113 from the catalytic domain forms an important hydrogen bond to Asn373, in the NAD(+)-binding domain. On glutamate binding, the side-chain of this lysine undergoes a significant movement in order to optimize its hydrogen bonding to the alpha-carboxyl group of the substrate. Despite this shift, the interaction between Lys113 and Asn373 is maintained by a large-scale conformational change that closes the cleft between the two domains. Modelling studies indicate that in this "closed" conformation the C-4 of the nicotinamide ring and the alpha-carbon atom of the amino acid substrate are poised for efficient hydride transfer. Examination of the structure has led to a proposal for the catalytic activity of the enzyme, which involves Asp165 as a general base, and an enzyme-bound water molecule, hydrogen-bonded to an uncharged lysine residue, Lys125, as an attacking nucleophile in the reaction. PubMed: 8263917DOI: 10.1006/jmbi.1993.1665 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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