Haem peroxidase

Peroxidase
Identifiers
Symbol	peroxidase
Pfam	PF00141
InterPro	IPR002016
PROSITE	PDOC00394
SCOP2	1hsr / SCOPe / SUPFAM
CDD	cd00314
Available protein structures: PDB   IPR002016 PF00141 (ECOD; PDBsum)   AlphaFold IPR002016 PF00141

Fungal peroxidase extension region
Identifiers
Symbol	Peroxidase_ext
Pfam	PF11895
InterPro	IPR024589
Available protein structures: PDB   IPR024589 PF11895 (ECOD; PDBsum)   AlphaFold IPR024589 PF11895

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${\displaystyle \rightleftharpoons }$ [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 ^[1] 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 ^[2] and Compound II, which can then oxidize a second substrate molecule.

Haem peroxidases include two superfamilies: one found in bacteria, fungi, and plants, and the second found in animals. The first one can be viewed as consisting of 3 major classes: ^[3]

• Class I, the intracellular peroxidases, includes: 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; ^[4] and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress. ^[5]
• 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. ^[6] 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. ^[7] 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.

Another family of haem peroxidases is the DyP-type peroxidase family. ^[8]

References

1. 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): 3438–3447. doi:10.1002/j.1460-2075.1994.tb06649.x. PMC   395246 . PMID   8062820.
2. Poulos TL, Li H (1994). "Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures". Structure. 2 (6): 461–464. doi:10.1016/S0969-2126(00)00046-0. PMID   7922023.
3. Welinder KG (1992). "Superfamily of plant, fungal and bacterial peroxidases". Curr. Opin. Struct. Biol. 2 (3): 388–393. doi:10.1016/0959-440X(92)90230-5.
4. Dalton DA (1991). "Ascorbate peroxidase". 2: 139–153.{{cite journal}}: Cite journal requires |journal= (help)
5. Welinder KG (1991). "Bacterial catalase-peroxidases are gene duplicated members of the plant peroxidase superfamily". Biochim. Biophys. Acta. 1080 (3): 215–220. doi:10.1016/0167-4838(91)90004-j. PMID   1954228.
6. Reddy CA, D Souza TM (1994). "Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium". FEMS Microbiol. Rev. 13 (2): 137–152. doi: 10.1111/j.1574-6976.1994.tb00040.x . PMID   8167033.
7. Campa A (1991). "Biological roles of plant peroxidases: known and potential function". 2: 25–50.{{cite journal}}: Cite journal requires |journal= (help)
8. 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): 223–33. doi:10.1002/prot.21550. PMID   17654545. S2CID   2845167.

This article incorporates text from the public domain Pfam and InterPro: IPR002016