title: Modeling and molecular dynamics of glutamine transaminase K/cysteine conjugate beta-lyase.
abstract: The homodimeric, pyridoxal 5'-phosphate (PLP)-dependent enzyme glutamine transaminase K/cysteine conjugate beta-lyase (GTK/beta-lyase) has been implicated in the bioactivation of chemopreventive compounds. This paper describes the first homology model of rat renal GTK/beta-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/beta-lyase, showed that the PLP-binding site of GTK/beta-lyase is highly conserved. Binding of the ligand alpha-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 pi-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/beta-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/beta-lyase may result in the rational design of new ligands and selective inhibitors.
authors.affiliation: Department of Pharmacochemistry, Division of Molecular Toxicology, Leiden/Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Venhorst
authors.forename: Antonius M
authors.initials: AM
authors.lastname: ter Laak
authors.forename: Moira
authors.initials: M
authors.lastname: Meijer
authors.forename: Ineke
authors.initials: I
authors.lastname: van de Wetering
authors.forename: Jan N M
authors.initials: JN
authors.lastname: Commandeur
authors.forename: Martijn
authors.initials: M
authors.lastname: Rooseboom
authors.forename: Nico P E
authors.initials: NP
authors.lastname: Vermeulen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D013437:Carbon-Sulfur Lyases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D004791:Enzyme Inhibitors / Q000378:metabolism; D007668:Kidney / Q000201:enzymology; D008024:Ligands; D008190:Lyases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011732:Pyridoxal Phosphate / Q000378:metabolism; D051381:Rats; D016415:Sequence Alignment; D015398:Signal Transduction; D000637:Transaminases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D014444:Tyrosine Transaminase / Q000378:metabolism
chemical_list: D004791:Enzyme Inhibitors; D008024:Ligands; D011732:Pyridoxal Phosphate; D000637:Transaminases; D014444:Tyrosine Transaminase; C427605:glutamine - phenylpyruvate transaminase; D008190:Lyases; D013437:Carbon-Sulfur Lyases; C019969:S-alkylcysteine lyase