Current Advances on Structure-Function Relationships of Pyridoxal 5'-Phosphate-Dependent Enzymes

Abstract

Pyridoxal 5'-phosphate (PLP) functions as a coenzyme in many enzymatic processes, including decarboxylation, deamination, transamination, racemization, and others. Enzymes, requiring PLP, are commonly termed PLP-dependent enzymes, and they are widely involved in crucial cellular metabolic pathways in most of (if not all) living organisms. The chemical mechanisms for PLP-mediated reactions have been well elaborated and accepted with an emphasis on the pure chemical steps, but how the chemical steps are processed by enzymes, especially by functions of active site residues, are not fully elucidated. Furthermore, the specific mechanism of an enzyme in relation to the one for a similar class of enzymes seems scarcely described or discussed. This discussion aims to link the specific mechanism described for the individual enzyme to the same types of enzymes from different species with aminotransferases, decarboxylases, racemase, aldolase, cystathionine β-synthase, aromatic phenylacetaldehyde synthase, et al. as models. The structural factors that contribute to the reaction mechanisms, particularly active site residues critical for dictating the reaction specificity, are summarized in this review.

Keywords: amino acid residues; pyridoxal 5′-phosphate; reaction mechanism; reaction specificity; structure-function relationship.

Figure 1

Scheme depicting of examples of the reaction mechanisms catalyzed by PLP-dependent enzymes. Reaction mechanisms of decarboxylation, racemization, transamination, and α-elimination and replacement are shown (Watanabe et al., , ; Eliot and Kirsch, ; Toney, 2014).

Figure 2

Partial protein sequence alignment of aminotransferases, and the position of three conserved residues in the active site. Sequences of Homo sapiens kynurenine aminotransferase (Accession: NP_057312.1), Mycobacterium tuberculosis H37Rv phenylalanine aminotransferase (PDB: 4R2N, chain A) (Nasir et al., 2016), Enterobacteriaceae L-histidinol phosphate aminotransferase (Accession: WP_000108941.1), Homo sapiens tyrosine aminotransferase (PDB: 3DYD, chain A) (http://www.rcsb.org/structure/3DYD) and Hordeum vulgare alanine aminotransferase (PDB: 3TCM, chain A) (Duff et al., 2012) are shown. The uncharged aromatic amino acid residues for π-π stacking with PLP ring are highlighted in blue box while the Asn and Tyr residues forming hydrogen bonds with PLP O3′ are highlighted in red boxes (A). The Asn and Tyr residues forming hydrogen bonds with O3′ of PLP are shown in green sticks while the ligands pyridoxamine phosphate (PMP), L-kynurenine and D-pyridoxyl-N,O-cycloserylamide-5-monophosphate (DCM) are shown in blue sticks. The uncharged aromatic amino acid residues forming π-π stacking with PLP pyridine ring and the Asp residue near pyridine ring N atom are also shown in green sticks. The distances between PLP O3′ and Asn or Tyr and the distances between pyridine ring N and Asp side chain are in blue dashed line and labeled (Unit: Å). L-kynurenine aminotransferase (PDB: 2R2N) (Han et al., 2008b) (B) and alanine aminotransferase (PDB: 3TCM) (Duff et al., 2012) (C) are presented as two examples.

Figure 3

The effect of protonation states of O3′ on delocalization. The stabilization of ionized O3′ (form I) through resonance structure (form II). The electron withdrawing effect of PLP with a neutral O3′ (form III) and formation of quinonoid intermediate (Toney, 2014) are shown.

Figure 4

Partial protein sequence alignment of aromatic amino acid decarboxylases, and the positions of the conserved His residue in aromatic amino acid decarboxylases. The conservation of His192 residue (residue number is from Drosophila melanogaster dopa decarboxylase) in Lactobacillus brevis tyrosine decarboxylase (PDB: 5HSJ, chain A) (Zhu et al., 2016), Ruminococcus Gnavus tryptophan decarboxylase (PDB: 4OBU, chain E) (Williams et al., 2014), Homo sapiens histidine decarboxylase (4E1O_A) (Komori et al., 2012), and Drosophila melanogaster dopa decarboxylase (Accession: NP_724164.1) is shown and is highlighted in red box (A). The dopa decarboxylase complexed with PLP and substrate-like inhibitor carbidopa [PDB: 1JS3 (Burkhard et al., 2001)] (B), the histidine decarboxylase complexed with PLP and substrate analog histidine-methyl-ester [PDB: 4E1O (Komori et al., 2012)] (C), and tryptophan decarboxylase complexed with PLP and substrate analog α-(fluoromethyl)-D-tryptophan [PDB: 4OBV (Williams et al., 2014)] (D) are shown. The external aldimines formed by PLP and substrate analogs are colored in blue and the conserved His residues in each decarboxylase critical for decarboxylation activity are shown in green sticks.

Figure 5

The mechanistic role of His192 residue in typical decarboxylation is shown (Liang et al., 2017).

Figure 6

Reaction mechanisms of alanine racemase and serine racemase (Watanabe et al., , ; Yoshimura and Goto, ; Goto et al., 2009).

Figure 7

Partial protein sequence alignment of plant and insect decarboxylases and aromatic acetaldehyde synthases. Catharanthus roseus tryptophan decarboxylase (P17770), Papaver somniferum tyrosine decarboxylase (AAC61842), Drosophila melanogaster dopa decarboxylase (NP_724164.1), Apis mellifera dopa decarboxylase (XP_394115.2), Arabidopsis thaliana aromatic acetaldehyde synthase (NP 849999), Rosa hybrid cultivar phenylacetaldehyde synthase (ABB04522.1), Apis mellifera 3,4-dihydroxyphenylacetaldehyde (DHPA) synthase, Drosophila melanogaster DHPA synthase (NP_724162.1) protein sequences are compared. The conservations of His vs. Asn residues at the equivalent position with His192 of Drosophila melanogaster dopa decarboxylase (NP_724164.1) are highlighted by red box. The conservations of flexible loop Tyr vs. Phe at the equivalent position with Tyr348 of Catharanthus roseus tryptophan decarboxylase (P17770) are highlighted by blue box.

Figure 8

The mechanistic role of Asn192 residue in Drosophila melanogaster DHPA synthase (Liang et al., 2017).