First crystal structure of an NADP+-dependent l-arginine dehydrogenase belonging to the μ-crystallin family

• Published in: International journal of biological macromolecules 2023-09, Vol.249, p.126070-126070, Article 126070
• Main Authors: Kawakami, Ryushi, Takami, Naoki, Hayashi, Junji, Yoneda, Kazunari, Ohmori, Taketo, Ohshima, Toshihisa, Sakuraba, Haruhiko
• Format: Article
• Language: English
• Subjects: Amino acid dehydrogenase; Crystal structure; l-Arginine dehydrogenase; Site-directed mutagenesis; μ-Crystallin/ornithine cyclodeaminase family
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2023.126070

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. •The crystal structure of an l-arginine dehydrogenase belonging to the μ-crystallin family was determined.•The substrate recognition residues of l-arginine dehydrogenase differ from those predicted for l-alanine dehydrogenase.•This study provides the first structural insight into the substrate binding mode of l-arginine dehydrogenase.