Summary: Peroxidase

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

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Haem peroxidase Edit Wikipedia article

Peroxidase

Identifiers

Symbol

peroxidase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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⁺ $\rightleftharpoons$ O]R' + substrate --> [Fe⁴⁺=O]R (Compound II) + oxidised substrate

[Fe⁴⁺ $\rightleftharpoons$ 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^[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]

[edit] References

^ 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): 3438â3447. PMC 395246. PMID 8062820. //www.ncbi.nlm.nih.gov/pmc/articles/PMC395246/.
^ Poulos TL, Li H (1994). "Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures". Structure 2 (6): 461â464. 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): 388â393. doi:10.1016/0959-440X(92)90230-5.
^ Dalton DA (1991). Ascorbate peroxidase. 2. pp. 139â153.
^ Welinder KG (1991). "Bacterial catalase-peroxidases are gene duplicated members of the plant peroxidase superfamily". Biochim. Biophys. Acta 1080 (3): 215â220. PMID 1954228.
^ Reddy CA, D Souza TM (1994). "Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium". FEMS Microbiol. Rev. 13 (2): 137â152. PMID 8167033.
^ Campa A (1991). Biological roles of plant peroxidases: known and potential function. 2. pp. 25â50.
^ 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): 223â33. 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 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

No Pfam abstract.

Internal database links

SCOOP:

DUF1669

External database links

HOMSTRAD:	peroxidase
PANDIT:	PF00141
PROSITE:	PDOC00394
Pseudofam:	PF00141
SCOP:	1hsr
SYSTERS:	peroxidase

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

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)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (162)	Full (7995)	Representative proteomes				NCBI (7388)	Meta (3647)
	Seed (162)	Full (7995)	RP15 (552)	RP35 (1714)	RP55 (2399)	RP75 (2881)	NCBI (7388)	Meta (3647)
Jalview	View	View	View	View	View	View	View	View
HTML	View		View	View	View	View
PP/heatmap	₁		View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (162)	Full (7995)	Representative proteomes				NCBI (7388)	Meta (3647)
	Seed (162)	Full (7995)	RP15 (552)	RP35 (1714)	RP55 (2399)	RP75 (2881)	NCBI (7388)	Meta (3647)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (162)	Full (7995)	Representative proteomes				NCBI (7388)	Meta (3647)
	Seed (162)	Full (7995)	RP15 (552)	RP35 (1714)	RP55 (2399)	RP75 (2881)	NCBI (7388)	Meta (3647)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

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 %

HMM information

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

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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family
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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

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

Cytochrom_C peroxidase

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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: peroxidase (PF00141)

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