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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.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Peroxidase Provide feedback
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002016
This entry represents the first type of haem peroxidases found in bacteria, fungi, plants.
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:
In this mechanism, the enzyme reacts with one equivalent of H 2 O 2 to give [Fe 4+ =O]R' (compound I). This is a two-electron oxidation/reduction reaction where H 2 O 2 is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl [ PUBMED:8062820 ] intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical [ PUBMED:7922023 ].
Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The first one can be viewed as consisting of 3 major classes. 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 [ PUBMED:1954228 ].
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, Mn 2+ serves as the reducing substrate [ PUBMED:8167033 ]. 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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||heme binding (GO:0020037)|
|peroxidase activity (GO:0004601)|
|Biological process||response to oxidative stress (GO:0006979)|
|oxidation-reduction process (GO:0055114)|
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Prosite; PfamB-105, Release 14.0;|
|Author:||Bateman A , Sonnhammer ELL , Studholme DJ|
|Number in seed:||156|
|Number in full:||31610|
|Average length of the domain:||242.70 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||73.43 %|
|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:||25|
|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 domain has been found. There are 761 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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