Genetic Alterations Shaping the Functional Properties of DyP Peroxidases

Abstract

Dye-decolorizing peroxidases (DyPs) represent a distinct family of heme peroxidases with unique capabilities in dye decolorization, lignin synthesis, and lignin degradation. While traditional phylogenetics and structural alignments have categorized DyPs into four distinct subclasses (A-D), the secret to unlocking their industrial versatility lies in the ability to understand and re-engineer the sophisticated architecture of their active sites. This review critically analyzed findings from 35 peer-reviewed articles (2007–2025) sourced from eight electronic databases, examining 93 distinct mutations within 20 different DyPs. Moving beyond basic classification, this study identifies hotspots that influence DyP performance, examining how site-directed mutagenesis affects structural integrity, H2O2 tolerance, and catalytic potential. Central among these is the histidine-arginine-aspartate (H-R-D) triad, which mediates the formation of high-valent intermediates in a class-specific manner. Analysis reveals that 29% of the studied variants surpassed their wild-type counterparts in catalytic efficiency, with a few variants achieving rare and desirable improvements in stability and an alkaline shift in optimal working pH. Mapping these mutational effects identifies the critical surface-exposed motifs and gatekeeping amino acids that govern long-range electron transfer and substrate accessibility. Since rate-limiting steps are substrate-dependent, a single mutation might produce diverse catalytic outcomes. Beyond clarifying structure–function relationships, these findings aim to provide a strategic blueprint for directed evolution. Identifying these catalytic hotspots guides the precision engineering of DyPs with tailored specificity and enhanced characteristics. Overall, this work acts as a catalyst for future protein engineering, unlocking a new era of robust biocatalysts capable of withstanding the harsh environments of modern industrial biotechnology.