7JX9

The crystal structure of human ornithine aminotransferase with an intermediate bound during inactivation by (1S,3S)-3-amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid.

Summary for 7JX9

• Entry DOI: 10.2210/pdb7jx9/pdb
• Descriptor: Ornithine aminotransferase, mitochondrial, (1S,3S,4S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-(1,1,3,3,3-pentafluoroprop-1-en-2-yl)cyclopentane-1-carboxylic acid, N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine, ... (4 entities in total)
• Functional Keywords: ornithine, aminotransferase, plp, mechanism-based inactivator, intermediate, irreversible inhibitor, transferase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 3
• Total formula weight: 136404.20

Authors

Butrin, A.,Beaupre, B.,Shen, S.,Silverman, R.B.,Moran, G.,Liu, D. (deposition date: 2020-08-26, release date: 2021-01-06, Last modification date: 2023-10-18)

Primary citation

Butrin, A.,Beaupre, B.A.,Kadamandla, N.,Zhao, P.,Shen, S.,Silverman, R.B.,Moran, G.R.,Liu, D.
Structural and Kinetic Analyses Reveal the Dual Inhibition Modes of Ornithine Aminotransferase by (1 S ,3 S )-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic Acid (BCF 3 ).
Acs Chem.Biol., 16:67-75, 2021

PubMed Abstract: Hepatocellular carcinoma (HCC) is the most common form of liver cancer and the leading cause of death among people with cirrhosis. HCC is typically diagnosed in advanced stages when tumors are resistant to both radio- and chemotherapy. Human ornithine aminotransferase (OAT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme involved in glutamine and proline metabolism. Because OAT is overexpressed in HCC cells and a contributing factor for the uncontrolled cellular division that propagates malignant tumors (Ueno et al. 2014, 61, 1080-1087), it is a potential drug target for the treatment of HCC. (1,3)-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid (BCF) has been shown in animal models to slow the progression of HCC by acting as a selective and potent mechanism-based inactivator of OAT (Zigmond et al. 2015, 6, 840-844). Previous studies have shown that the BCF-OAT reaction has a bifurcation in which only 8% of the inhibitor inactivates the enzyme while the remaining 92% ultimately acts as a substrate and undergoes hydrolysis to regenerate the active PLP form of the enzyme. In this manuscript, the rate-limiting step of the inactivation mechanism was determined by stopped-flow spectrophotometry and time-dependent F NMR experiments to be the decay of a long-lived external aldimine species. A crystal structure of this transient complex revealed both the structural basis for fractional irreversible inhibition and the principal mode of inhibition of OAT by BCF, which is to trap the enzyme in this transient but quasi-stable external aldimine form.

PubMed: 33316155
DOI: 10.1021/acschembio.0c00728

Experimental method

X-RAY DIFFRACTION (1.96 Å)