Homology models of two isozymes of manganese peroxidase: Prediction of a Mn(II) binding site

Abstract

The three-dimensional structures of two isozymes of manganese peroxidase (MnP) have been predicted from homology modeling using lignin peroxidase as a template. Although highly homologous, MnP differs from LiP by the requirement of Mn(II) as an intermediate in its oxidation of substrates. The Mn(II) site is absent in LiP and unique to the MnP family of peroxidases. The model structures were used to identify the unique Mn(II) binding sites, to determine to what extent they were conserved in the two isozymes, and to provide insight into why this site is absent in LiP. For each isozyme of MnP, three candidate Mn(II) binding sites were identified. Energy optimizations of the three possible Mn(II) enzyme complexes allowed the selection of the most favorable Mn(II) binding site as one with the most anionic oxygen moieties best configured to act as ligands for the Mn(II). At the preferred site, the Mn(II) is coordinated to the carboxyl oxygens of Glu-35, Glu-39, and Asp-179, and a propionate group of the heme. The predicted Mn(II) binding site is conserved in both isozymes. Comparison between the residues at this site in MnP and the corresponding residues in LiP shows that two of the three anionic residues in MnP are replaced by neutral residues in LiP, explaining why LiP does not bind Mn(II).

Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii

“…5. Homology models for other peroxidases, including P. chrysosporium LiP (Du et al ., 1992) and MnP (Johnson et al ., 1994), had been reported, and they provided useful information on enzyme architecture and spatial arrangement of amino acid residues.…”

“…In the model for P. eryngii peroxidase MnPL, Mn 2+ could be co‐ordinated by carboxylate oxygens of E36, E40 and D175 and the internal propionate of haem. A similar binding site, including two water molecules to complete Mn 2+ hexa‐co‐ordination, was postulated in both theoretical (Johnson et al ., 1994) and crystal models (Sundaramoorthy et al ., 1994) of P. chrysosporium MnP1, and was then confirmed by site‐directed mutagenesis (Sundaramoorthy et al ., 1997). LiP from P. chrysosporium presents different residues at these positions (see Fig.…”

Description of a Versatile Peroxidase Involved in the Natural Degradation of Lignin That Has Both Manganese Peroxidase and Lignin Peroxidase Substrate Interaction Sites

“…Other enzymes could oxidize Mn 2ϩ via superoxide anion radical, such as that generated by redox cycling (47). The existence of a Mn 2ϩ binding site in P. chrysosporium MnP was predicted in theoretical models of the enzyme built by sequence homology using LiP as a template (48), as well as in the first crystal structure obtained (16 Fig. 3).…”

A new versatile peroxidase from Pleurotus

“…The Mn-interaction site of MnP constitutes one exception. Although Mn2+ oxidation at the haem edge had been suggested [37], an Mn-interaction site near the internal haem propionate was first postulated in theoretical [38] and crystal models [26] and then confirmed by site-directed muta-genesis (SDM) and X-ray diffraction of MnP/ Mn2+ complexes [39][40][41]. As shown in Fig.…”