Crystal structure and characterization of a novel l-serine ammonia-lyase from Rhizomucor miehei

l-serine ammonia-lyase, as a member of the β-family of pyridoxal-5′-phosphate (PLP) dependent enzymes, catalyzes the conversion of l-serine (l-threonine) to pyruvate (α-ketobutyrate) and ammonia. The crystal structure of l-serine ammonia-lyase from Rhizomucor miehei (RmSDH) was solved at 1.76 Å resolution by X-ray diffraction method. The overall structure of RmSDH had the characteristic β-family PLP dependent enzyme fold. It consisted of two distinct domains, both of which show the typical open twisted α/β structure. A PLP cofactor was located in the crevice between the two domains, which was attached to Lys52 by a Schiff-base linkage. Unique residue substitutions (Gly78, Pro79, Ser146, Ser147 and Thr312) were discovered at the catalytic site of RmSDH by comparison of structures of RmSDH and other reported eukaryotic l-serine ammonia-lyases. Optimal pH and temperature of the purified RmSDH were 7.5 and 40 °C, respectively. It was stable in the pH range of 7.0–9.0 and at temperatures below 40 °C. This is the first crystal structure of a fungal l-serine ammonia-lyase. It will be useful to study the catalytic mechanism of β-elimination enzymes and will provide a basis for further enzyme engineering. [Display omitted] •The crystal structure of a fungal l-serine ammonia-lyase (RmSDH) was solved.•Five unique residue substitutions are found at the catalytic site of RmSDH.•RmSDH was expressed in Pichia. pastoris and biochemically characterized.•RmSDH has potential application in splitting d/l-serine.