Chlorite Dismutases, DyPs, and EfeB: 3 Microbial Heme Enzyme Families Comprise the CDE Structural Superfamily

Abstract

Heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. The chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic ClO 2 − , a function believed to have evolved only in the last few decades. Family members have since been found in fifteen bacterial and archaeal genera, suggesting ancient roots. A structure-and sequence-based examination of the family is presented, in which key sequence and structural motifs are identified and possible functions for family proteins are proposed. Newly identified structural homologies moreover demonstrate clear connections to two other large, ancient, and functionally mysterious protein families. We propose calling them collectively the CDE superfamily of heme proteins.

First Crystal Structure of a Fungal High-redox Potential Dye-decolorizing Peroxidase

“…It has been reported that acidic side chains in the vicinity of a tryptophan or a tyrosine stabilize an emerging radical cation (26,47,48). Alignments with other DyPs show that Tyr-337 is a conserved residue in fungal as well as bacterial DyPs and the related enzymes TyrA from Shewanella oneidensis and EfeB from Escherichia coli but is missing in Cld-like proteins (5).…”

“…As a result, a new family of enzymes was established to accommodate these unusual peroxidases (4). From a structural viewpoint, DyPs are best considered members of a highly diverse superfamily of proteins comprising, among others, Clds and DyPs, sharing a ferredoxin-like core of ␤-sheets as a common feature (5). Actually, even the term "DyP" circumscribes a polyphyletic group that can be roughly divided into four different entities.…”

“…Research on bacterial members has been comparatively more extensive. A native crystal structure was needed to substantiate recent results involving fungal as well as bacterial DyP-type peroxidases (5,12). To gain further insight into the structural properties of the eucaryotic (in this case fungal) DyPs, AauDyPI from the jelly fungus A. auricula-judae (Auriculariales, Basidiomycota) was purified and crystallized, and the crystal structure was determined at 2.1 Å resolution (Protein Data Bank (PDB) code 4AU9).…”

The Chlorite Dismutase (HemQ) from Staphylococcus aureus Has a Redox-sensitive Heme and Is Associated with the Small Colony Variant Phenotype

“…SaHemQ is representative of a large subgroup of Cld-family proteins, including all Clds from phylum Firmicutes, which have a conserved glutamine residue at the position of a distal Arg that we have observed is critical for efficient reactivity with anionic oxidants (1,3,8). Unlike typical peroxidases, Clds likewise lack a distal base and other residues important for stabilizing polar reaction intermediates ( Fig.…”

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

“…The peroxidase-chlorite dismutase superfamily (CDE structural superfamily) comprises chlorite dismutases (Clds), chlorite dismutase-like (Cld-like) proteins (HemQs in Gram-positive bacteria) and dye-decolourizing peroxidases (DyPs) [1,2]. Although distinct enzymatic reactions can be assigned to Clds (degradation of chlorite to chloride and dioxygen) and DyPs (H 2 O 2 -mediated one-electron oxidation reactions of various aromatic compounds), knowledge about the biochemical and physiological function of Cld-like proteins is only fragmentary at present.…”