Crystal structure of a novel type of ornithine δ-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii

• Published in: International journal of biological macromolecules 2022-05, Vol.208, p.731-740
• Main Authors: Kawakami, Ryushi, Ohshida, Tatsuya, Hayashi, Junji, Yoneda, Kazunari, Furumoto, Toshio, Ohshima, Toshihisa, Sakuraba, Haruhiko
• Format: Article
• Language: English
• Subjects: Archaea; Crystal structure; Ornithine aminotransferase
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2022.03.114

Ornithine δ-aminotransferase (Orn-AT) activity was detected for the enzyme annotated as a γ-aminobutyrate aminotransferase encoded by PH1423 gene from Pyrococcus horikoshii OT-3. Crystal structures of this novel archaeal ω-aminotransferase were determined for the enzyme in complex with pyridoxal 5′-phosphate (PLP), in complex with PLP and l-ornithine (l-Orn), and in complex with N-(5′-phosphopyridoxyl)-l-glutamate (PLP-l-Glu). Although the sequence identity was relatively low (28%), the main-chain coordinates of P. horikoshii Orn-AT monomer showed notable similarity to those of human Orn-AT. However, the residues recognizing the α-amino group of l-Orn differ between the two enzymes. In human Orn-AT, Tyr55 and Tyr85 recognize the α-amino group, whereas the side chains of Thr92* and Asp93*, which arise from a loop in the neighboring subunit, form hydrogen bonds with the α-amino group of the substrate in P. horikoshii enzyme. Site-directed mutagenesis suggested that Asp93* plays critical roles in maintaining high affinity for the substrate. This study provides new insight into the substrate binding of a novel type of Orn-AT. Moreover, the structure of the enzyme with the reaction-intermediate analogue PLP-l-Glu bound provides the first structural evidence for the “Glu switch” mechanism in the dual substrate specificity of Orn-AT. •The crystal structures of a novel archaeal type of ornithine δ-aminotransferase were determined.•The substrate recognition residues of this enzyme are notably different from those of human ornithine δ-aminotransferase.•This study provides the first structural evidence for the “Glu switch” mechanism of ornithine δ-aminotransferase.