Diversity of structures, catalytic mechanisms and processes of cofactor biosynthesis of tryptophylquinone-bearing enzymes

Abstract

Tryptophyquinone-bearing enzymes contain protein-derived cofactors formed by posttranslational modifications of Trp residues. Tryptophan tryptophylquinone (TTQ) is comprised of a di-oxygenated Trp residue, which is cross-linked to another Trp residue. Cysteine tryptophylquinone (CTQ) is comprised of a di-oxygenated Trp residue, which is cross-linked to a Cys residue. Despite the similarity of these cofactors, it has become evident in recent years that the overall structures of the enzymes that possess these cofactors vary, and that the gene clusters that encode the enzymes are quite diverse. While it had been long assumed that all tryptophylquinone enzymes were dehydrogenases, recently discovered classes of these enzymes are oxidases. A common feature of enzymes that have these cofactors is that the posttranslational modifications that form the mature cofactors are catalyzed by a modifying enzyme. However, it is now clear that modifying enzymes are different for different tryptophylquinone enzymes. For methylamine dehydrogenase a di-heme enzyme, MauG, is needed to catalyze TTQ biosynthesis. However, no gene similar to mauG is present in the gene clusters that encode the other enzymes, and the recently characterized family of CTQ-dependent oxidases, termed LodA-like proteins, require a flavoenzyme for cofactor biosynthesis.

Keywords: Amine dehydrogenase; Amine oxidase; Posttranslational modification; Quinoprotein; Redox cofactor; Tryptophan.

Figure 1.

Tryptophan tryptophylquinone (TTQ) and cysteine tryptophylquinone (CTQ). The posttranslational modifications of the residues are shown in red and R indicated point on the protein where the residues are attached.

Figure 2.

(A) AADH from Alcaligenes faecalis (PDB ID: 2AH1) and (B) MADH from Paracoccus denitrificans (PDB ID: 3SWS with the MauG chains omitted) with the α and β subunits shown as blue and green cartoon, respectively. The TTQ cofactors are shown as spheres. (C) QHNDH from Paracoccus denitrificans (PDB ID: 1JJU) with the α, β and γ subunits shown as pink, blue and green cartoon, respectively. The CTQ and heme cofactors are shown as spheres. Stick representations of the quinone cofactors from AADH (D), MADH (E) and QHNDH (F) showing interactions at < 3.5 Å with protein residues shown as sticks, water molecules shown as red spheres or a Na⁺ shown as a purple sphere.

Figure 3.

(A) Alignment of GoxA from Pseudoalteromonas luteoviolaceae (blue, PDB ID: 6BYW) and LodA from Marinomonas mediterranea (gold, PDB ID: 3WEU). The homotetrameric assembly of LodA (B) and GoxA (C) are presented with subunits shown in shades of blue and green. Intersubunit interactions in GoxA (D) illustrate how the CTQ active site is closed versus the open active site of LodA (E). Subunits are shown in shades of blue.

Figure 4.

Reaction mechanism of MADH. Only a portion of the TTQ cofactor is shown. B indicates and active site base.

Figure 5.

Gene clusters which encode different enzymes with TTQ or CTQ cofactors. These are the genes present in MADH from P. denitrificans [22], AADH from Alcalgenes faecalis [31], QHNDH from P. denitrificans [32], LodA from M. mediteranea [35], and GoxA from M. mediteranea [34]. The quinone-bearing gene products are indicated in red and the known modifying enzymes are indicated in blue.

Figure 6.

(A) Crystal structure of the MauG-preMADH complex (PDB ID: 3L4M). MauG is shown in pink, α-MADH in blue and β-MADH in green cartoon. Important residues and cofactors are shown as sticks colored according to element. Structure of the preMADH site (B), the cross-linked intermediate (PDB ID: 3FAN) (C) and the mature TTQ cofactor (PDB ID: 3FA1) (D).

Figure 7.

Other protein-derived carbonyl cofactors. The posttranslational modifications of the residues are shown in red and R indicates point on the protein where the residues are attached.