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398  structures 2016  species 2  interactions 7995  sequences 39  architectures

Family: peroxidase (PF00141)

Summary: Peroxidase

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This is the Wikipedia entry entitled "Haem peroxidase". More...

Haem peroxidase Edit Wikipedia article

Peroxidase
Identifiers
Symbol peroxidase
Pfam PF00141
InterPro IPR002016
PROSITE PDOC00394
SCOP 1hsr
SUPERFAMILY 1hsr
CDD cd00314

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 \rightleftharpoons [Fe4+=O]R' (Compound I) + H2O
[Fe4+\rightleftharpoonsO]R' + substrate --> [Fe4+=O]R (Compound II) + oxidised substrate
[Fe4+\rightleftharpoonsO]R + substrate --> Fe3+ + H2O + oxidised 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 where H2O2 is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl[1] 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.[2]

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.[3] 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;[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. 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. pp. 139–153. 
  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. pp. 25–50. 
  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. 

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

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This tab holds annotation information from the InterPro database.

InterPro entry IPR002016

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) + oxidised substrate [Fe4+=O]R + substrate --> Fe3+ + H2O + oxidised 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 where H2O2 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 [PUBMED:]. 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, Mn2+ 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.

Gene Ontology

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Domain organisation

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(162)
Full
(7995)
Representative proteomes NCBI
(7388)
Meta
(3647)
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(552)
RP35
(1714)
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(2399)
RP75
(2881)
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  Seed
(162)
Full
(7995)
Representative proteomes NCBI
(7388)
Meta
(3647)
RP15
(552)
RP35
(1714)
RP55
(2399)
RP75
(2881)
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  Seed
(162)
Full
(7995)
Representative proteomes NCBI
(7388)
Meta
(3647)
RP15
(552)
RP35
(1714)
RP55
(2399)
RP75
(2881)
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Seed source: Prosite; PfamB-105, Release 14.0;
Previous IDs: none
Type: Family
Author: Bateman A, Sonnhammer ELL, Studholme DJ
Number in seed: 162
Number in full: 7995
Average length of the domain: 260.20 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 77.65 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 19.9 20.0
Model length: 230
Family (HMM) version: 18
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Interactions

There are 2 interactions for this family. More...

peroxidase Cytochrom_C

Structures

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 398 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 seqence.

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