The peroxidase database
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Classes

Non Animal peroxidase superfamily: Class II

  Contact author: Christophe Dunand

  Last update: 2017-04-28 (Marcel Zamocky)

Lignin-modifying class II heme peroxidases
-Lignin peroxidase (LiP)
-Manganese peroxidase (MnP)
-Versatile peroxidase (VP)
-Other class II peroxidase (CII)

Profiles

Pfam: PF00141
Interpro: IPR010255 Haem peroxidase and IPR002016 Haem peroxidase, plant/fungal/bacterial
The profiles do not make distinction between animal and non animal peroxidase and between the different non animal peroxidase classes

Class II peroxidase
InterPro: IPR001621 Fungal lignin peroxidase


Description Fungal ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs), are extracellular haem enzymes involved in the degradation of lignin. Lignin is the second most abundant organic compound on Earth and its biodegradation is slow. Certain fungi are able extensively to decompose all the important structural components of wood, including both cellulose and lignin.The first step in lignin degradation is depolymerisation, catalysed by the LiPs (ligninases). LiPs are secreted, along with hydrogen peroxide (H2O2), by white-rot fungi under conditions of nutrient limitation.
3D structures have been determined for LiP and MnP from Phanerochaete chrysosporium (White-rot fungus), and for the fungal peroxidase from Arthromyces ramosus. All these proteins share the same architecture and consist of 2 all-alpha domains, between which is embedded the haem group. The helical topography of LiPs is nearly identical to that of yeast CcP.
Class II peroxidases (unlike Class I and like Class III) are glycosylated and contain calcium ions and disulfide bridges as well as a peptide signal directing the protein to the endoplasmic reticulum for secretion.

Lignin Peroxidase (LiP, EC 1.11.1.14): LiP attacks lignin bonds directly. Contains a W residu conserved.

Manganese Peroxidase (MnP, EC 1.11.1.13): In MnP, Mn2+ serves as the reducing substrate. MnP takes an electron from Mn(II), resulting in Mn(III) that diffuses from the enzyme surface and attacks lignin. Keys residus for Mn oxidation (ExxxE and D).

Versatile Peroxidase (VP): Multifunctional peroxidases sharing the catalytic properties of LiP and MnP. The protein sequences present keys residus for Mn oxidation (ExxxE and D) as well as the conserved W.

Ancestral Lignin Peroxidase (CII): Protein sequences found at the origin of the "lignin tree". Keys residus for Mn oxidation (ExxxE and D) as well as the conserved W are missing. The sequences have a shorter C-Term.

New CII Peroxidase (CII): Proteins mainly present in Ascomycota (plant pathogen). Keys residus for Mn oxidation (ExxxE and D) as well as the conserved W are missing. Also referred as "generic peroxidases" in Floudas et al. 2012

FOLy (Fungal Oxidative Lignin enzYme) a database that describes oxidases potentially involved in the degradation of lignin and including class II peroxidases can bring complementary information.
Literature Morgenstern I, Klopman S, Hibbett DS. Molecular evolution and diversity of lignin degrading heme peroxidases in the Agaricomycetes. J Mol Evol. 2008 Mar;66(3):243-57. PMID: 18292958

Reddy CA , D. Souza TM Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium. FEMS Microbiol. Rev. 13 137-152 1994 PMID: 8167033

Poulos TL , Edwards SL , Wariishi H , Gold MH Crystallographic refinement of lignin peroxidase at 2 A. J. Biol. Chem. 268 4429-4440 1993 PMID: 8440725

Lundell TK, Mäkelä MR, Hildén K.Lignin-modifying enzymes in filamentous basidiomycetes--ecological, functional and phylogenetic review. J Basic Microbiol. 2010 Feb;50(1):5-20. PMID: 20175122

Sundaramoorthy M. , Kishi K. , Gold M.H. , Poulos T.L. The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06-A resolution. J. Biol. Chem. 269 32759-32767 1994 PMID: 7806497

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