Molecular modeling of manganese peroxidase from the lignin-degrading fungus Ceriporiopsis subvermispora   and structural comparison with other peroxidases

Ceriporiopsis subvermispora

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is a white-rot basidiomycete that produces several isoenzymes of manganese peroxidase (MnP•). A cDNA of one of them (MnP13-1) has been isolated and sequenced. The deduced aminoacid sequence shows about 60% similarity with the MnPs from Phanerochaete chrysosporium

. Based on the crystal structures of MnP and lignin peroxidase (LiP) from P. chrysosporium, and of a peroxidase from Arthromyces ramosus

(ARP), we have modeled by homology the three dimensional structure of MnP13-1 using standard modeling procedures. Local molecular mechanics optimization performed in the region corresponding to the binding sites of Ca²⁺ and Mn²⁺ in MnP13-1 demonstrated that the stereochemistry and the geometry of binding are conserved in both MnPs. A putative aromatic binding site in MnP13-1 is described. We also report structural differences between the two MnPs, arising from the insertion in MnP13-1 of the sequences TGGN between residues S230 and D231 and TDSP at the C-terminal, both of which may have functional significance.

Keywords
Lignin peroxidase, Manganese peroxidase, Molecular modeling, Sequence alignment, Structural comparison