7LNM

Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclopentene-1-carboxylic acid

7LNM の概要

• エントリーDOI: 10.2210/pdb7lnm/pdb
• 分子名称: Ornithine aminotransferase, mitochondrial, (1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid (3 entities in total)
• 機能のキーワード: ornithine aminotransferase, oat, aminotransferase, inactivator, inhibitor, transferase, transferase-inactivator complex, transferase/inactivator
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 271395.78

構造登録者

Butrin, A.,Catlin, D.,Zhu, W.,Liu, D.,Silverman, R. (登録日: 2021-02-07, 公開日: 2021-08-25, 最終更新日: 2023-10-18)

主引用文献

Zhu, W.,Doubleday, P.F.,Butrin, A.,Weerawarna, P.M.,Melani, R.D.,Catlin, D.S.,Dwight, T.A.,Liu, D.,Kelleher, N.L.,Silverman, R.B.
Remarkable and Unexpected Mechanism for ( S )-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase.
J.Am.Chem.Soc., 143:8193-8207, 2021

PubMed Abstract: Human ornithine aminotransferase (OAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that was recently found to play an important role in the metabolic reprogramming of hepatocellular carcinoma (HCC) via the proline and glutamine metabolic pathways. The selective inhibition of OAT by compound exhibited potent antitumor activity. Inspired by the discovery of the aminotransferase inactivator (1,3)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid (), we rationally designed, synthesized, and evaluated a series of six-membered-ring analogs. Among them, was identified as a new selective OAT inactivator, which demonstrated a potency 22× greater than that of . Three different types of protein mass spectrometry approaches and two crystallographic approaches were employed to identify the structure of OAT- and the formation of a remarkable final adduct () in the active site. These spectral studies reveal an enzyme complex heretofore not observed in a PLP-dependent enzyme, which has covalent bonds to two nearby residues. Crystal soaking experiments and molecular dynamics simulations were carried out to identify the structure of the active-site intermediate and elucidate the order of the two covalent bonds that formed, leading to . The initial covalent reaction of the activated warhead occurs with *Thr322 from the second subunit, followed by a subsequent nucleophilic attack by the catalytic residue Lys292. The turnover mechanism of by OAT was supported by a mass spectrometric analysis of metabolites and fluoride ion release experiments. This novel mechanism for OAT with will contribute to the further rational design of selective inactivators and an understanding of potential inactivation mechanisms by aminotransferases.

PubMed: 34014654
DOI: 10.1021/jacs.1c03572

実験手法

X-RAY DIFFRACTION (2 Å)