Summary: Fungal peroxidase extension region
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This is the Wikipedia entry entitled "Haem peroxidase". More...
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Haem peroxidase Edit Wikipedia article
|SCOPe||1hsr / SUPFAM|
|Fungal peroxidase extension region|
Haem peroxidases (or heme peroxidases) are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme:
- Fe3+ + H2O2 [Fe4+=O]R' (Compound I) + H2O
- [Fe4+=O]R' + substrate --> [Fe4+=O]R (Compound II) + oxidized substrate
- [Fe4+=O]R + substrate --> Fe3+ + H2O + oxidized substrate
In this mechanism, the enzyme reacts with one equivalent of H2O2 to give [Fe4+=O]R' (compound I). This is a two-electron oxidation/reduction reaction in which H2O2 is reduced to water and the enzyme is oxidized. One oxidizing equivalent resides on iron, giving the oxyferryl intermediate, and in many peroxidases the porphyrin (R) is oxidized to the porphyrin pi-cation radical (R'). Compound I then oxidizes an organic substrate to give a substrate radical and Compound II, which can then oxidize a second substrate molecule.
- Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants; and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress.
- Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn2+ serves as the reducing substrate. Class II proteins contain four conserved disulphide bridges and two conserved calcium-binding sites.
- Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole-3-acetic acid (IAA) catabolism; ethylene biosynthesis; and so on. Class III proteins are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes.
The crystal structures of a number of these proteins show that they share the same architecture - two all-alpha domains between which the haem group is embedded.
- Nelson RE, Fessler LI, Takagi Y, Blumberg B, Keene DR, Olson PF, Parker CG, Fessler JH (1994). "Peroxidasin: a novel enzyme-matrix protein of Drosophila development". EMBO J. 13 (15): 3438â€“3447. PMC 395246. PMID 8062820.
- Poulos TL, Li H (1994). "Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures". Structure. 2 (6): 461â€“464. doi:10.1016/S0969-2126(00)00046-0. PMID 7922023.
- Welinder KG (1992). "Superfamily of plant, fungal and bacterial peroxidases". Curr. Opin. Struct. Biol. 2 (3): 388â€“393. doi:10.1016/0959-440X(92)90230-5.
- Dalton DA (1991). "Ascorbate peroxidase". 2: 139â€“153. Cite journal requires
- Welinder KG (1991). "Bacterial catalase-peroxidases are gene duplicated members of the plant peroxidase superfamily". Biochim. Biophys. Acta. 1080 (3): 215â€“220. doi:10.1016/0167-4838(91)90004-j. PMID 1954228.
- Reddy CA, D Souza TM (1994). "Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium". FEMS Microbiol. Rev. 13 (2): 137â€“152. doi:10.1111/j.1574-6976.1994.tb00040.x. PMID 8167033.
- Campa A (1991). "Biological roles of plant peroxidases: known and potential function". 2: 25â€“50. Cite journal requires
- Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (November 2007). "Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif". Proteins. 69 (2): 223â€“33. doi:10.1002/prot.21550. PMID 17654545.
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Fungal peroxidase extension region Provide feedback
This region is found as an extension to a haem peroxidase domain in some fungi. This region is about 80 amino acids in length and forms an extended structure on the surface of the peroxidase domain PF00141.
This tab holds annotation information from the InterPro database.
InterPro entry IPR024589
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Peroxidases are found in bacteria, fungi, plants and animals. Fungal ligninases are extracellular haem enzymes involved in the degradation of lignin. They include lignin peroxidases (LiPs), manganese-dependent peroxidases (MnPs) and versatile peroxidases, which combine the substrate-specificity characteristics of the other two [ PUBMED:10187820 ]. In MnP, Mn 2+ serves as the reducing substrate [ PUBMED:8167033 ].
It is commonly thought that the plant polymer lignin is the second most abundant organic compound on Earth, exceeded only by cellulose. Higher plants synthesise vast quantities of insoluble macromolecules, including lignins. Lignin is an amorphous three-dimensional aromatic biopolymer composed of oxyphenylpropane units. Biodegradation of lignins is slow - it is probable that their decomposition is the rate-limiting step in the biospheric carbon-oxygen cycle, which is mediated almost entirely by the catabolic activities of microorganisms. The white-rot fungi are able extensively to decompose all the important structural components of wood, including both cellulose and lignin. Under the proper environmental conditions, white-rot fungi completely degrade all structural components of lignin, with ultimate formation of CO 2 and H 2 O. The first step in lignin degradation is depolymerisation, catalysed by the LiPs (ligninases). LiPs are secreted, along with hydrogen peroxide (H 2 O 2 ), by white-rot fungi under conditions of nutrient limitation. The enzymes are not only important in lignin biodegradation, but are also potentially valuable in chemical waste disposal because of their ability to degrade environmental pollutants [ PUBMED:8167033 ].
To date, 3D structures have been determined for LiP [ PUBMED:8440725 ] and MnP [ PUBMED:7806497 ] from Phanerochaete chrysosporium (White-rot fungus), and for the fungal peroxidase from Arthromyces ramosus [ PUBMED:8289254 ]. 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 cytochrome c peroxidase (CCP) [ PUBMED:7922023 ], despite the former having four disulphide bonds, which are absent in CCP (MnP has an additional disulphide bond at the C terminus).
This C-terminal domain is found in fungal ligninases. It is about 80 amino acids in length and forms an extended structure on the surface of the peroxidase domain INTERPRO .
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Key: available, not generated, — not available.
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|Seed source:||PFAM-B_1962 (release 23.0)|
|Author:||Assefa S , Coggill P , Bateman A|
|Number in seed:||25|
|Number in full:||618|
|Average length of the domain:||75.30 aa|
|Average identity of full alignment:||43 %|
|Average coverage of the sequence by the domain:||21.25 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peroxidase_ext domain has been found. There are 82 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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