Abstract
Ganoderma lucidum is a basidiomycete fungus that produces ligninase for the modification of lignin. Lignin peroxidase (LiP) is a glycoprotein that acts on the recalcitrant cell wall component lignin. In the present study, the phylogenetic analysis of Ganoderma lucidum GD88 with the partial coding sequence (cds) of other LiP isoforms was performed using MEGA6. After determination of the open reading frame, the +3 frame nucleotide sequence was converted to protein using the EMBOSS Transseq and the secondary structure was predicted using the Chou and Fasman Secondary Structure Prediction server (CFSSP). Protein modeling was also performed by SWISS-MODEL. The obtained result shows that the lipH partial cds of Ganoderma lucidum GD88 is homologous to the lipD gene of Phanerochaete chrysosporium. The secondary structure prediction result revealed that the percent content of the helix (67) is higher than the percent contents of sheet (53.4) and turns (13.6). According to the generated model, LiP H protein is a homodimer with chains A and B. The heme acts as a ligand and plays a major role in structure stabilization.
Highlights
Fungi are a very good source of lignin peroxidase, and the white rot fungi are the best-known producers of lignolytic enzymes (Kirk and Farrell, 1987), followed by brown and soft rot fungi (Niladevi, 2009)
The actinomycetes are potent producers of ligninolytic enzymes, and extracellular lignin peroxidase has been identified in different strains of Streptomyces, such as S. viridosporus, S. chromofuscus and S. psammoticus (Ramachandra et al, 1987; Pasti et al, 1990; Niladevi and Prema, 2005)
Lignin peroxidase (EC 1.11.14) is a heme-containing lignin-modifying enzyme secreted by basidiomycete filamentous fungi and can degrade the recalcitrant cell wall component lignin
Summary
Fungi are a very good source of lignin peroxidase, and the white rot fungi are the best-known producers of lignolytic enzymes (Kirk and Farrell, 1987), followed by brown and soft rot fungi (Niladevi, 2009). In the present study we describe the structure of LiP H isolated from Ganoderma lucidum GD88 by prediction and modeling tools. The partial coding sequences of other LiP isoforms were accessed from the NCBI database.
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