7VO1

Structure of aminotransferase-substrate complex

Summary for 7VO1

• Entry DOI: 10.2210/pdb7vo1/pdb
• Descriptor: 454aa long hypothetical 4-aminobutyrate aminotransferase, N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid (3 entities in total)
• Functional Keywords: protein-plp-substrate complex, transferase
• Biological source: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
• Total number of polymer chains: 2
• Total formula weight: 102118.90

Authors

Sakuraba, H.,Ohshida, T.,Ohshima, T. (deposition date: 2021-10-12, release date: 2022-03-30, Last modification date: 2023-11-29)

Primary citation

Kawakami, R.,Ohshida, T.,Hayashi, J.,Yoneda, K.,Furumoto, T.,Ohshima, T.,Sakuraba, H.
Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.
Int.J.Biol.Macromol., 208:731-740, 2022

PubMed Abstract: 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.

PubMed: 35337912
DOI: 10.1016/j.ijbiomac.2022.03.114

Experimental method

X-RAY DIFFRACTION (2.99 Å)