Plant Copper Metalloenzymes As Prospects for New Metabolism Involving Aromatic Compounds

Abstract

Copper is an important transition metal cofactor in plant metabolism, which enables diverse biocatalysis in aerobic environments. Multiple classes of plant metalloenzymes evolved and underwent genetic expansions during the evolution of terrestrial plants and, to date, several representatives of these copper enzyme classes have characterized mechanisms. In this review, we give an updated overview of chemistry, structure, mechanism, function and phylogenetic distribution of plant copper metalloenzymes with an emphasis on biosynthesis of aromatic compounds such as phenylpropanoids (lignin, lignan, flavonoids) and cyclic peptides with macrocyclizations via aromatic amino acids. We also review a recent addition to plant copper enzymology in a copper-dependent peptide cyclase called the BURP domain. Given growing plant genetic resources, a large pool of copper biocatalysts remains to be characterized from plants as plant genomes contain on average more than 70 copper enzyme genes. A major challenge in characterization of copper biocatalysts from plant genomes is the identification of endogenous substrates and catalyzed reactions. We highlight some recent and future trends in filling these knowledge gaps in plant metabolism and the potential for genomic discovery of copper-based enzymology from plants.

Keywords: biocatalysis; biosynthesis; copper; copper enzyme; plant metabolism.

FIGURE 1

Representative metabolic reactions catalyzed by plant copper metalloenzymes. (A) Oxidative phenol coupling by laccase. (B) Enediol oxidation by ascorbate oxidase. (C) o-Diphenol oxidation by catechol oxidase and tyrosinase. (D) Phenol monooxygenation and o-diphenol oxidation by aurone synthase and tyrosinase. (E) Phenol monooxygenation by larreatricin hydroxylase. (F) Oxidative deamination by N-methylputrescine oxidase. (G) Superoxide dismutation by Cu, Zn-superoxide dismutase. (H) Peptide macrocyclizations by BURP domain cyclase.

FIGURE 2

Structure of a plant laccase. (A) Protein structure of maize laccase ZmLac3 (PDB ID: 6KLG) (Xie et al., 2020). The three domains are highlighted in magenta, green and blue, the copper atoms are shown as brown spheres and disulfide bonds as yellow sticks. (B) Copper center of ZmLac3 laccase with T1 and TNC copper atoms and corresponding copper-binding residues. A water or hydroxide molecule is shown as a red sphere. Copper coordination is highlighted by yellow dashed lines. (C) Catalytic mechanism of laccase with catalytic cycle highlighted by red arrows and reduction of resting state (RO) or decay of native intermediate (NI) state to resting state highlighted by black arrows. Adapted with permission from Augustine et al. (2010; Copyright 2010 American Chemical Society).

FIGURE 3

Structure of a plant ascorbate oxidase. (A) Protein structure model of zucchini ascorbate oxidase (PDB ID: 1AOZ) (Messerschmidt et al., 1992). The three domains are highlighted in magenta, green and blue, the copper atoms are shown as brown spheres. (B) Copper center of zucchini ascorbate oxidase with T1 and TNC copper atoms and corresponding copper-binding residues. A water or hydroxide molecule is shown as a red sphere. Copper coordination is highlighted by yellow dashed lines.

FIGURE 4

Structures and mechanism of plant type III polyphenol oxidases. (A) Protein structure of active form of sweet potato catechol oxidase IpCO (PDB: 1BT1) (Klabunde et al., 1998). (B) T3 copper center of sweet potato catechol oxidase IpCO. (C) Protein structure of active walnut tyrosinase JrTYR (PDB ID: 5CE9) (Bijelic et al., 2015). (D) Protein structure of latent aurone synthase CgAUS (PDB: 4Z11) (Molitor et al., 2016). C-terminal shielding domain is highlighted in dark gray. (E) T3 copper center of walnut tyrosinase JrTYR. (F) Catalytic mechanism of monophenolase reaction (inner cycle) and diphenolase reaction (outer cycle) in plant type III polyphenol oxidases. Adapted with permission from Solomon et al. (2014; Copyright 2014 American Chemical Society). In PPO protein structures, α-helices are highlighted in green, β-sheets in blue, disulfide bonds in yellow, copper atoms are brown spheres and water or hydroxides are red spheres. Copper coordination is highlighted in copper center figures by yellow dashed lines.

FIGURE 5

Structure and mechanism of a plant copper-dependent amine oxidase. (A) Homodimer protein structure of pea copper-dependent amine oxidase (PDB ID: 1KSI) (Kumar et al., 1996). (B) Monomer structure of pea CuAO. (C) T2 copper center with copper-binding residues and TPQ cofactor. Copper coordination is highlighted by yellow dashed lines. (D) Proposed mechanism of TPQ biogenesis. Adapted with permission from Dubois and Klinman (2005; Copyright 2005 Elsevier). (E) Proposed catalytic mechanism of CuAO. Adapted with permission from Mills et al. (2019; Copyright 2019 Springer Nature). In panels (A,B), the three domains D2, D3, and D4 are highlighted in magenta, green, and cyan, respectively. In panels (A–C), copper atoms are shown as brown spheres, manganese atoms as purple spheres, water molecules as red spheres.

FIGURE 6

Structure of a plant Cu,Zn-superoxide dismutase. (A) Protein structure of spinach Cu,Zn-superoxide dismutase (PDB ID: 1SRD) (Kitagawa and Katsube, 1994). (B) T2 copper center of spinach Cu,Zn-SOD. Copper coordination is highlighted by yellow dashed lines. In panels (A,B), α-helices are highlighted in green, β-sheets are highlighted in blue. Copper atoms are shown as brown spheres, zinc atoms as purple spheres. (C) Proposed catalytic mechanism of Cu,Zn-SOD. Adapted with permission from Tainer et al. (1983; Copyright 1983 Springer Nature).

FIGURE 7

Primary structure of BURP domain peptide cyclases. (A) Characterized core peptide substrate sequences of known BURP domain peptide cyclases and characterized tyrosine- or tryptophan-derived macrocyclization sites (1–3). (B) Primary structures of representatives of the two general types of BURP domain cyclases and corresponding peptide natural products. In the BURP domain sequence, core peptides corresponding to the natural product are highlighted in red, the BURP domain sequence is underlined, the BURP domain-defining residues are highlighted in blue. (C) Two models of autocatalysis for BURP domain-based peptide macrocyclization.

FIGURE 8

Structure of a plant plastocyanin. (A) Protein structure of poplar plastocyanin (PDB: 1PLC) (Guss et al., 1992). (B) T1 copper center of poplar plastocyanin. In panels (A,B), α-helices are highlighted in green, β-sheets are highlighted in blue. Copper atoms are shown as brown spheres.

FIGURE 9

Strategies for characterization of copper metalloenzymes from plant genomes.