Computational investigation of the histidine ammonia-lyase reaction: a modified loop conformation and the role of the zinc(II) ion
Résumé
Possible reaction intermediates of the histidine ammonia-lyase (HAL) reaction were investigated within the tightly closed active site of HAL from (HAL). The closed structure of HAL was derived from the crystal structure of HAL inhibited with -cysteine, in which the 39-80 loop including the catalytically essential Tyr53 was replaced. This modified loop with closed conformation was modeled using the structure of phenylalanine ammonia-lyase from (PAL) with a tightly closed active site as a template. Three hypothetical structures of the covalently bound intermediate in the HAL active site were investigated by conformational analysis. The distances between the acidic β-hydrogen of the ligand and the appropriate oxygen atoms of Tyr53, Ty280 and Glu414 − which may act as enzymic bases − in the conformations of the three hypothetical intermediate structures were analyzed together with the substrate and product arrangements. The calculations indicated that the most plausible HAL reaction pathway involves the -MIO intermediate structure in which the -histidine substrate is covalently bound to the -3,5-dihydro-5-methylidene-4-imidazol-4-one (MIO) prosthetic group of the apoenzyme the amino group. Density functional theory (DFT) calculations − on a truncated model of the MIO intermediate containing a Zn ion coordinated to the imidazole ring of the ligand and to His83, Met382 and a water molecule − indicated that Zn-complex formation plays a role in the reactivity and substrate specificity of HAL.
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