The enzyme is a member of the ammonia lyase family, which cleaves carbon–nitrogen bonds. Like other lyases, PAL requires only one substrate for the forward reaction, but two for the reverse. It is thought to be mechanistically similar to the related enzyme histidine ammonia-lyase (EC:4.3.1.3, HAL).[8] The systematic name of this enzyme class is L-phenylalanine ammonia-lyase (trans-cinnamate-forming). Previously, it was designated as EC 4.3.1.5, but that class has been redesignated as EC 4.3.1.24 (phenylalanine ammonia-lyases), EC 4.3.1.25 (tyrosine ammonia-lyases), and EC 4.3.1.26 (phenylalanine/tyrosine ammonia-lyases). Other names in common use include tyrase, phenylalanine deaminase, tyrosine ammonia-lyase, L-tyrosine ammonia-lyase, phenylalanine ammonium-lyase, PAL, and L-phenylalanine ammonia-lyase.
The cofactor3,5-dihydro-5-methyldiene-4H-imidazol-4-one (MIO) is involved in the reaction and sits atop the positive pole of three polar helices in the active site, which helps to increase its electrophilicity.[12] MIO is attacked by the aromatic ring of L-phe, which activates the C-H bond on the β carbon for deprotonation by a basic residue.[13][14] The carbanionintermediate of this E1cB-elimination reaction, which is stabilized by partial positive regions in the active site, then expels ammonia to form the cinnamate alkene. The mechanism of the reaction of PAL is thought to be similar to the mechanism of the related enzyme histidine ammonia lyase.[13]
Proposed autocatalytic formation of MIO cofactor from the tripeptide Ala-Ser-Gly by two water elimination steps.[15]
A dehydroalanine residue was long thought to be the key electrophilic catalytic residue in PAL and HAL, but the active residue was later found instead to be MIO, which is even more electrophilic.[16][17] It is formed by cyclization and dehydration of conserved Ala-Ser-Gly tripeptide segment. The first step of MIO formation is a cyclization-elimination by an intramolecular nucleophilic attack of the nitrogen of Gly204 at the carbonyl group of Ala202. A subsequent water elimination from the side chain of Ser203 completes the system of crossconjugated double bonds.[15] Numbers are given for the phenylalanine ammonia lyase from Petroselinumcrispum (PDB 1W27). Although MIO is a polypeptide modification, it was proposed to call it a prosthetic group, because it has the quality of an added organic compound.[8]
Phenylalanine ammonia lyase is composed of four identical subunits composed mainly of alpha-helices, with pairs of monomers forming a single active site.[17] Catalysis in PAL may be governed by the dipole moments of seven different alpha helices associated with the active site.[19] The active site contains the electrophilic group MIO non-covalently bonded to three helices. Leu266, Asn270, Val269, Leu215, Lys486, and Ile472 are located on the active site helices, while Phe413, Glu496, and Gln500 contribute to the stabilization of the MIO cofactor. The orientation of dipole moments generated by helices within the active site generates an electropositive region for ideal reactivity with MIO. The partially positive regions in the active site may also help stabilize the charge of a carbanion intermediate. PAL is structurally similar to the mechanistically related histidine ammonia lyase, although PAL has approximately 215 additional residues.[17]
Enzyme substitution therapy using PAL to treat phenylketonuria (PKU), an autosomal recessive genetic disorder in humans in which mutations in the phenylalanine hydroxylase (PAH, EC 1.14.16.1) gene inactivate the enzyme is being explored.[6] This leads to an inability of the patient to metabolize phenylalanine, causing elevated levels of Phe in the bloodstream (hyperphenylalaninemia) and mental retardation if therapy is not begun at birth.[6]
The reverse reaction catalyzed by PAL has been explored for use to convert trans-cinnamic acid to L-phenylalanine, which is a precursor of the sweetener aspartame. This process was developed by Genex Corporation but was never commercially adopted.[23]
Unnatural amino acid synthesis
Analogous to how aspartame is synthesized, PAL is also used to synthesize unnatural amino acids from various substitutedcinnamic acids for research purposes.[24]Steric hindrance from arene substitution limits PAL's utility for this purpose however.[25] For instance, when Rhodotorula glutinis was used to affect this biotransformation the enzyme was discovered to be intolerant of all para substituents other than fluorine, presumably due to the element's small atomic radius. Meta and ortho positions were found to be more tolerant, but still limited by, larger substituents. For instance the enzyme's active site permitted orthomethoxy substitution but forbade metaethoxy. Other organisms with different versions of the enzyme may be less limited in this way.[26][27]
Structural studies
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1T6J, 1T6P, 1W27, 1Y2M, and 2NYF.
^Hahlbrock K, Grisebach H (1 June 1979). "Enzymic Controls in the Biosynthesis of Lignin and Flavonoids". Annual Review of Plant Physiology. 30 (1): 105–130. doi:10.1146/annurev.pp.30.060179.000541.
^ abcSarkissian CN, Gámez A (December 2005). "Phenylalanine ammonia lyase, enzyme substitution therapy for phenylketonuria, where are we now?". Molecular Genetics and Metabolism. 86 (Suppl 1): S22-6. doi:10.1016/j.ymgme.2005.06.016. PMID16165390.
^Evans C, Hanna K, Conrad D, Peterson W, Misawa M (1 February 1987). "Production of phenylalanine ammonia-lyase (PAL): isolation and evaluation of yeast strains suitable for commercial production of L-phenylalanine". Applied Microbiology and Biotechnology. 25 (5): 406–414. doi:10.1007/BF00253309. S2CID40066810.
^ abSchwede TF, Rétey J, Schulz GE (April 1999). "Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile". Biochemistry. 38 (17): 5355–61. doi:10.1021/bi982929q. PMID10220322.
^Alunni S, Cipiciani A, Fioroni G, Ottavi L (April 2003). "Mechanisms of inhibition of phenylalanine ammonia-lyase by phenol inhibitors and phenol/glycine synergistic inhibitors". Archives of Biochemistry and Biophysics. 412 (2): 170–5. doi:10.1016/s0003-9861(03)00007-9. PMID12667480.
^Rétey, János (2003). "Discovery and role of methylidene imidazolone, a highly electrophilic prosthetic group". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1647 (1–2): 179–184. doi:10.1016/S1570-9639(03)00091-8. PMID12686130.
^ abcCalabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T (September 2004). "Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis". Biochemistry. 43 (36): 11403–16. doi:10.1021/bi049053+. PMID15350127.
^Sato T, Kiuchi F, Sankawa U (1 January 1982). "Inhibition of phenylalanine ammonia-lyase by cinnamic acid derivatives and related compounds". Phytochemistry. 21 (4): 845–850. Bibcode:1982PChem..21..845S. doi:10.1016/0031-9422(82)80077-0.
