8J1C

Structure of amino acid dehydrogenase in complex with NADP

Summary for 8J1C

• Entry DOI: 10.2210/pdb8j1c/pdb
• Descriptor: Ornithine cyclodeaminase family protein, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, LYSINE, ... (6 entities in total)
• Functional Keywords: dehydrogenase, oxidoreductase
• Biological source: Pseudomonas veronii
• Total number of polymer chains: 4
• Total formula weight: 146790.90

Authors

Sakuraba, H.,Ohshima, T. (deposition date: 2023-04-12, release date: 2023-08-16)

Primary citation

Kawakami, R.,Takami, N.,Hayashi, J.,Yoneda, K.,Ohmori, T.,Ohshima, T.,Sakuraba, H.
First crystal structure of an NADP + -dependent l-arginine dehydrogenase belonging to the mu-crystallin family.
Int.J.Biol.Macromol., 249:126070-126070, 2023

PubMed Abstract: Crystal structures of Pseudomonas veroniil-arginine dehydrogenase (l-ArgDH), belonging to the μ-crystallin/ornithine cyclodeaminase family, were determined for the enzyme in complex with l-lysine and NADP and with l-arginine and NADPH. The main chain coordinates of the P. veroniil-ArgDH monomer showed notable similarity to those of Archaeoglobus fulgidusl-AlaDH, belonging to the same family, and pro-R specificity similar to l-AlaDH for hydride transfer to NADP was postulated. However, the residues recognizing the α-amino group of the substrates differed between the two enzymes. Based on a substrate modeling study, it was proposed that in A. fulgidusl-AlaDH, the amino group of l-alanine interacts via a water molecule (W510) with the side chains of Lys41 and Arg52. By contrast, the α-amino group of l-arginine formed hydrogen bonds with the side chains of Thr224 and Asn225 in P. veroniil-ArgDH. Moreover, the guanidino group of l-arginine was fixed into the active site via hydrogen bonds with the side chain of Asp54. Site-directed mutagenesis suggested that Asp54 plays an important role in maintaining high reactivity against the substrate and that Tyr58 and Lys71 play critical roles in enzyme catalysis.

PubMed: 37524275
DOI: 10.1016/j.ijbiomac.2023.126070

Experimental method

X-RAY DIFFRACTION (2.2 Å)