Modeling and molecular dynamics of glutamine transaminase K/cysteine conjugate β-lyase

Abstract

The homodimeric, pyridoxal 5′-phosphate (PLP)-dependent enzyme glutamine transaminase K/cysteine conjugate β-lyase (GTK/β-lyase) has been implicated in the bioactivation of chemopreventive compounds. This paper describes the first homology model of rat renal GTK/β-lyase and its active site residues, deduced from molecular dynamics (MD) simulations of the binding mode of 13 structurally diverse cysteine S-conjugates and amino acids after Amber-parametrization of PLP. Comparison with Thermus thermophilus aspartate aminotransferase (tAAT) and Trypanosoma cruzi tyrosine aminotransferase (tTAT), used as templates for modeling GTK/β-lyase, showed that the PLP-binding site of GTK/β-lyase is highly conserved. Binding of the ligand α-carboxylate-group occurred via the conserved residues Arg 432 and Asn 219, and Asn 50 and Gly 70. Two pockets accommodated the various ligand side chains. A small pocket, located directly above PLP, was of a highly hydrophobic and aromatic character. A larger pocket, formed partly by the substrate access channel, was more hydrophilic and notably involved the salt bridge partners Glu 54 and Arg 99∗ (∗ denotes the other subunit). Ligand-binding residues included Leu 51, Phe 71, Tyr 135, Phe 373 and Phe 312∗, and π-stacking interactions were often observed. Tyr 135 and Asn 50 were prominent in hydrogen bonding with the sulfur-atom of cysteine S-conjugates. The observed binding mode of the ligands corresponded well with their experimentally determined inhibitory potency toward GTK/β-lyase. The current homology model thus provides a starting point for further validation of the role of active site residues in ligand-binding by means of mutagenesis studies. Ultimately, insight in the binding of ligands to GTK/β-lyase may result in the rational design of new ligands and selective inhibitors.