5VWR

E.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP)-alpha-ketoglutarate

Summary for 5VWR

• Entry DOI: 10.2210/pdb5vwr/pdb
• Related: 5VWO 5VWQ
• Descriptor: Aspartate aminotransferase, (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid, GLYCEROL, ... (4 entities in total)
• Functional Keywords: aspartate aminotransferase, mechanism-based inactivator, ketimine, (1r, 3s, 4s)-3-amino-4-fluorocyclopentane-1-carboxylic acid (fcp), alpha-ketoglutarate, transferase
• Biological source: Escherichia coli (strain K12)
• Cellular location: Cytoplasm: P00509
• Total number of polymer chains: 1
• Total formula weight: 44455.94

Authors

Mascarenhas, R.,Liu, D.,Le, H.,Silverman, R. (deposition date: 2017-05-22, release date: 2017-09-13, Last modification date: 2024-03-13)

Primary citation

Mascarenhas, R.,Le, H.V.,Clevenger, K.D.,Lehrer, H.J.,Ringe, D.,Kelleher, N.L.,Silverman, R.B.,Liu, D.
Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.
Biochemistry, 56:4951-4961, 2017

PubMed Abstract: Potent mechanism-based inactivators can be rationally designed against pyridoxal 5'-phosphate (PLP)-dependent drug targets, such as ornithine aminotransferase (OAT) or γ-aminobutyric acid aminotransferase (GABA-AT). An important challenge, however, is the lack of selectivity toward other PLP-dependent, off-target enzymes, because of similarities in mechanisms of all PLP-dependent aminotransferase reactions. On the basis of complex crystal structures, we investigate the inactivation mechanism of OAT, a hepatocellular carcinoma target, by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP), a known inactivator of GABA-AT. A crystal structure of OAT and FCP showed the formation of a ternary adduct. This adduct can be rationalized as occurring via an enamine mechanism of inactivation, similar to that reported for GABA-AT. However, the crystal structure of an off-target, PLP-dependent enzyme, aspartate aminotransferase (Asp-AT), in complex with FCP, along with the results of attempted inhibition assays, suggests that FCP is not an inactivator of Asp-AT, but rather an alternate substrate. Turnover of FCP by Asp-AT is also supported by high-resolution mass spectrometry. Amid existing difficulties in achieving selectivity of inactivation among a large number of PLP-dependent enzymes, the obtained results provide evidence that a desirable selectivity could be achieved, taking advantage of subtle structural and mechanistic differences between a drug-target enzyme and an off-target enzyme, despite their largely similar substrate binding sites and catalytic mechanisms.

PubMed: 28816437
DOI: 10.1021/acs.biochem.7b00499

Experimental method

X-RAY DIFFRACTION (1.72 Å)