Structural Basis for the Entrance into the Phenylpropanoid Metabolism Catalyzed by Phenylalanine Ammonia-Lyase

Abstract

Because of its key role in secondary phenylpropanoid metabolism, Phe ammonia-lyase is one of the most extensively studied plant enzymes. To provide a basis for detailed structure–function studies, the enzyme from parsley (Petroselinum crispum) was crystallized, and the structure was elucidated at 1.7-Å resolution. It contains the unusual electrophilic 4-methylidene-imidazole-5-one group, which is derived from a tripeptide segment in two autocatalytic dehydration reactions. The enzyme resembles His ammonia-lyase from the general His degradation pathway but contains 207 additional residues, mainly in an N-terminal extension rigidifying a domain interface and in an inserted α-helical domain restricting the access to the active center. Presumably, Phe ammonia-lyase developed from His ammonia-lyase when fungi and plants diverged from the other kingdoms. A pathway of the catalyzed reaction is proposed in agreement with established biochemical data. The inactivation of the enzyme by a nucleophile is described in detail

Discovery of Two Cyanobacterial Phenylalanine Ammonia Lyases: Kinetic and Structural Characterization,

“…The eukaryotic PALs are distinguished structurally from the prokaryotic ammonia lyases by their larger size, which results primarily from the 54-residue N-terminal extension, the inserted shielding domain and some other small inserted segments (10). Based on structural and sequence homology, the prokaryotic PALs and TALs are proposed to have evolved from bacterial HAL.…”

“…Interestingly, although the cyanobacterial PALs are more similar in size to the bacterial HAL (all of the bacterial ammonia lyases lack two polypeptide segments present in the eukaryotic PALs, a long N-terminal extension and an additional domain occurring near the C-terminus), the cyanobacterial PALs are more similar structurally to yeast and parsley PAL. The additional domain, termed the shielding domain (10), represents an insertion in the polypeptide chain of the eukaryotic PALs immediately after the helical bundle. In these PALs, the first α-helix of the shielding domain extends helix-5 of the core bundle, whereas in the cyanobacterial PALs, the much shorter helix-5 is followed by a small connecting segment that leads immediately into the peripheral α-helices of the C-terminal domain (Figure 2).…”

“…In TAL, the first of these segments is packed tightly within the active-site cleft and interacts closely with the bound substrate/product molecule, whereas the second segment forms a more external loop that caps the active-site region. These loops appear to be intrinsically flexible in the PAL proteins, as they are also poorly ordered in the structures of parsley and yeast PAL (9,10). In the crystal structures of the cyanobacterial PALs, the active-site cleft appears very exposed to the external solvent, and the absence of stabilizing interactions contributed by the disordered inner loop is a likely reason for the failure to observe stable binding to these PALs of the substrate (L-Phe), the product (cinnamic acid), and a potent PAL-specific inhibitor (2-aminoindan-2-phosphonic acid) (31).…”

Structure and function of enzymes involved in the biosynthesis of phenylpropanoids

“…It is also the only general phenylpropanoid pathway enzyme for which detailed structure-function information is available. The first structures of bacterial and plant PALs were solved in 2004 [10,55]. Other bacterial and fungal PAL/TAL structures were elucidated more recently [45,47].…”

Ecological and Functional Evaluation of Species Candidate for Heavy Metals Phytoremediation in SIN Porto Torres (Sardinia, Italy)

“…The enzyme phenylalanine ammonia lyase (PAL) catalyzes deamination reaction of the amino acid phenyl alanine at the gateway from the primary metabolism into the important secondary phenylpropanoid / phenolic metabolism in plants. Effects of different stresses on PAL activity has been previously reported [27][28][29][30][31][32]. Regulation of PAL activity in plants is complex, as there are multiple PAL encoding genes, some of which are expressed only in specific tissues or only under certain environmental conditions [33].…”