Identification and structural characterization of heme binding in a novel dye‐decolorizing peroxidase, TyrA

Abstract

TyrA is a member of the dye-decolorizing peroxidase (DyP) family, a new family of heme-dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 A. TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold. Both domains contribute to the heme-binding site. Co-crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases.

Molecular Characterization of a Novel Peroxidase from the Cyanobacterium Anabaena sp. Strain PCC 7120

“…This feature has been observed in bacterial DyPs that are predominantly oligomeric (29,41,42) compared to the largely monomeric secretory fungal DyPs (13, 15, 18). (27).…”

“…However, with the exception of a DyP from the plant pathogenic fungus T. cucumeris Dec1 (an anamorph of Rhizoctonia solani, a very common fungal plant pathogen), which has been characterized extensively (18,28,(30)(31)(32)34), little information is available on other members of the DyP family. In particular, studies on bacterial DyPs have been limited to only the automatically translated sequence or structural data (41,42). Within the context of further understanding the structure-function and potential applicability of these novel types of enzymes in general, we have taken an interest in DyP-type enzymes, particularly, the less known bacterial groups.…”

Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact

“…The enzymatic reaction could involve a distortion of the tetrapyrrol ring, as it is achieved by ferrochelatase during metal insertion (25). However, in the heme-TyrA structure (a YfeX ortholog), the protoporphyrin ring is plane (26).…”

Ligands in crystal structures that aid in functional characterization

“…Subsequent structures of complexes with heme (PDB code 2d3q, T. Sato, Y. Sugano & M. Shoda, unpublished work; PDB code 2iiz (Zubieta, Joseph et al, 2007) allowed the first unambiguous characterization of the active site, including the basis of the observed low-pH activity and the relationship between heme binding and oligomerization (Zubieta, Joseph et al, 2007). Identification of the active site from this liganded structure also allowed analysis of substrate specificity, which appears to be tailored to small hydrophobic molecules and is consistent with the putative role of TyrA in melanin biosynthesis.…”