Heme-dependent peroxidases superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	All alpha proteins [ 46456] (284)
Fold:	Heme-dependent peroxidases [ 48112]
Superfamily:	Heme-dependent peroxidases [ 48113] (3)
Families:	CCP-like [ 48114] (4)
	Catalase-peroxidase KatG [ 74753]
	Myeloperoxidase-like [ 48132] (2)

Superfamily statistics

	Genomes (1,129)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	10,777	15,496	113
Proteins	9,666	11,978	104

Functional annotation

General category	Metabolism
Detailed category	Redox

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)

	GO term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	developmental process	1.745e-05	2.287e-07	Least Informative	Direct
Biological Process (BP)	response to stimulus	4.719e-06	1.414e-11	Least Informative	Direct
Biological Process (BP)	multicellular organismal process	0.001511	3.606e-08	Least Informative	Inherited
Biological Process (BP)	localization	0.02154	0.6008	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	0.02468	0.3738	Least Informative	Inherited
Biological Process (BP)	ion transport	7.207e-07	0.0001535	Moderately Informative	Direct
Biological Process (BP)	multi-organism process	0.002155	5.286e-08	Moderately Informative	Inherited
Biological Process (BP)	response to oxygen-containing compound	0.005036	1.581e-10	Moderately Informative	Inherited
Biological Process (BP)	cellular response to stress	0.01823	0.007374	Moderately Informative	Inherited
Biological Process (BP)	anatomical structure morphogenesis	0.0004747	0.7426	Moderately Informative	Inherited
Biological Process (BP)	cell differentiation	0.9037	0.9359	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	0.0007003	0.001969	Moderately Informative	Inherited
Biological Process (BP)	organ development	0.2683	1	Moderately Informative	Inherited
Biological Process (BP)	response to abiotic stimulus	0.0002363	0.1877	Moderately Informative	Inherited
Biological Process (BP)	tissue development	0.001297	0.3239	Moderately Informative	Inherited
Biological Process (BP)	response to inorganic substance	2.065e-05	4.228e-07	Informative	Direct
Biological Process (BP)	metal ion transport	1.385e-08	6.737e-05	Informative	Direct
Biological Process (BP)	nitrogen compound transport	1.92e-06	7.141e-06	Informative	Direct
Biological Process (BP)	response to external stimulus	0.08867	0.8129	Informative	Inherited
Biological Process (BP)	defense response	0.7259	0.03843	Informative	Inherited
Biological Process (BP)	response to other organism	0.02083	4.364e-06	Informative	Inherited
Biological Process (BP)	anion transport	0.05333	0.001475	Informative	Inherited
Biological Process (BP)	epithelium development	0.02419	0.4094	Informative	Inherited
Biological Process (BP)	epidermis development	4.836e-09	2.816e-08	Highly Informative	Direct
Biological Process (BP)	inorganic anion transport	5.183e-05	2.48e-05	Highly Informative	Direct
Biological Process (BP)	response to fungus	0.002244	0.002536	Highly Informative	Inherited
Biological Process (BP)	cellular response to starvation	0.00122	0.04796	Highly Informative	Inherited
Biological Process (BP)	response to osmotic stress	0.007674	0.1099	Highly Informative	Inherited
Molecular Function (MF)	oxidoreductase activity	9.821e-07	0	Moderately Informative	Direct
Molecular Function (MF)	peroxidase activity	0	0	Highly Informative	Direct
Cellular Component (CC)	intracellular organelle part	0.6208	1	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.08057	0.5943	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.02293	0.05637	Least Informative	Inherited
Cellular Component (CC)	vacuole	1.701e-05	5.201e-06	Informative	Direct
Cellular Component (CC)	external encapsulating structure	0	0	Informative	Direct
Cellular Component (CC)	plastid	0.0002822	0.01769	Informative	Inherited
Cellular Component (CC)	cell junction	2.259e-07	0.01021	Informative	Inherited
Cellular Component (CC)	symplast	1.203e-09	3.451e-06	Highly Informative	Direct
Cellular Component (CC)	cell-cell junction	4.05e-08	0.001684	Highly Informative	Inherited
Cellular Component (CC)	cell wall	0	0.1308	Highly Informative	Inherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)

	GO term	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	biosynthetic process	0.0001965	Least Informative	Direct
Biological Process (BP)	multicellular organismal process	3.606e-08	Least Informative	Direct
Biological Process (BP)	developmental process	2.287e-07	Least Informative	Direct
Biological Process (BP)	single-organism metabolic process	9.527e-09	Least Informative	Direct
Biological Process (BP)	response to stimulus	1.414e-11	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	1	Least Informative	Inherited
Biological Process (BP)	cellular aromatic compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	0.9333	Least Informative	Inherited
Biological Process (BP)	localization	0.6008	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	0.3738	Least Informative	Inherited
Biological Process (BP)	ion transport	0.0001535	Moderately Informative	Direct
Biological Process (BP)	lipid biosynthetic process	7.391e-12	Moderately Informative	Direct
Biological Process (BP)	cellular lipid metabolic process	7.27e-07	Moderately Informative	Direct
Biological Process (BP)	small molecule biosynthetic process	7.394e-09	Moderately Informative	Direct
Biological Process (BP)	multi-organism process	5.286e-08	Moderately Informative	Direct
Biological Process (BP)	cellular response to chemical stimulus	7.027e-09	Moderately Informative	Direct
Biological Process (BP)	response to oxygen-containing compound	1.581e-10	Moderately Informative	Direct
Biological Process (BP)	cellular catabolic process	0.277	Moderately Informative	Inherited
Biological Process (BP)	organic hydroxy compound metabolic process	0.001255	Moderately Informative	Inherited
Biological Process (BP)	cellular amino acid metabolic process	0.005403	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	0.001969	Moderately Informative	Inherited
Biological Process (BP)	cellular response to stress	0.007374	Moderately Informative	Inherited
Biological Process (BP)	regulation of response to stimulus	0.9836	Moderately Informative	Inherited
Biological Process (BP)	response to organic substance	1	Moderately Informative	Inherited
Biological Process (BP)	signal transduction	0.6283	Moderately Informative	Inherited
Biological Process (BP)	response to endogenous stimulus	0.007936	Moderately Informative	Inherited
Biological Process (BP)	anatomical structure morphogenesis	0.7426	Moderately Informative	Inherited
Biological Process (BP)	cell differentiation	0.9359	Moderately Informative	Inherited
Biological Process (BP)	organ development	1	Moderately Informative	Inherited
Biological Process (BP)	response to abiotic stimulus	0.1877	Moderately Informative	Inherited
Biological Process (BP)	tissue development	0.3239	Moderately Informative	Inherited
Biological Process (BP)	system process	0.1532	Moderately Informative	Inherited
Biological Process (BP)	monocarboxylic acid metabolic process	0.005764	Moderately Informative	Inherited
Biological Process (BP)	immune system process	0.004375	Moderately Informative	Inherited
Biological Process (BP)	cellular modified amino acid metabolic process	5.825e-05	Informative	Direct
Biological Process (BP)	fatty acid metabolic process	4.85e-10	Informative	Direct
Biological Process (BP)	response to oxidative stress	5.107e-08	Informative	Direct
Biological Process (BP)	blood circulation	0	Informative	Direct
Biological Process (BP)	response to inorganic substance	4.228e-07	Informative	Direct
Biological Process (BP)	response to organic nitrogen	0.0003535	Informative	Direct
Biological Process (BP)	response to organic cyclic compound	3.067e-06	Informative	Direct
Biological Process (BP)	metal ion transport	6.737e-05	Informative	Direct
Biological Process (BP)	response to cytokine stimulus	1.84e-07	Informative	Direct
Biological Process (BP)	response to other organism	4.364e-06	Informative	Direct
Biological Process (BP)	nitrogen compound transport	7.141e-06	Informative	Direct
Biological Process (BP)	monocarboxylic acid biosynthetic process	6.613e-08	Informative	Direct
Biological Process (BP)	response to external stimulus	0.8129	Informative	Inherited
Biological Process (BP)	cellular response to oxygen-containing compound	0.2199	Informative	Inherited
Biological Process (BP)	regulation of growth	0.01189	Informative	Inherited
Biological Process (BP)	regulation of hormone levels	0.0034	Informative	Inherited
Biological Process (BP)	regulation of response to stress	0.01521	Informative	Inherited
Biological Process (BP)	anion transport	0.001475	Informative	Inherited
Biological Process (BP)	epithelium development	0.4094	Informative	Inherited
Biological Process (BP)	defense response	0.03843	Informative	Inherited
Biological Process (BP)	immune effector process	0.05473	Informative	Inherited
Biological Process (BP)	transition metal ion transport	2.247e-05	Highly Informative	Direct
Biological Process (BP)	regulation of blood pressure	0	Highly Informative	Direct
Biological Process (BP)	epidermis development	2.816e-08	Highly Informative	Direct
Biological Process (BP)	response to purine-containing compound	7.835e-15	Highly Informative	Direct
Biological Process (BP)	inorganic anion transport	2.48e-05	Highly Informative	Direct
Biological Process (BP)	phenol-containing compound metabolic process	1.658e-06	Highly Informative	Direct
Biological Process (BP)	cytokine-mediated signaling pathway	1.348e-14	Highly Informative	Direct
Biological Process (BP)	unsaturated fatty acid metabolic process	1.174e-11	Highly Informative	Direct
Biological Process (BP)	cellular response to reactive oxygen species	8.904e-11	Highly Informative	Direct
Biological Process (BP)	response to hydrogen peroxide	0.0002181	Highly Informative	Direct
Biological Process (BP)	icosanoid biosynthetic process	0	Highly Informative	Direct
Biological Process (BP)	response to fungus	0.002536	Highly Informative	Inherited
Biological Process (BP)	regulation of multi-organism process	0.002622	Highly Informative	Inherited
Biological Process (BP)	hydrogen peroxide metabolic process	0.0489	Highly Informative	Inherited
Biological Process (BP)	cellular response to starvation	0.04796	Highly Informative	Inherited
Biological Process (BP)	response to osmotic stress	0.1099	Highly Informative	Inherited
Molecular Function (MF)	binding	1	Least Informative	Inherited
Molecular Function (MF)	oxidoreductase activity	0	Moderately Informative	Direct
Molecular Function (MF)	organic cyclic compound binding	0.03501	Moderately Informative	Inherited
Molecular Function (MF)	heterocyclic compound binding	0.02977	Moderately Informative	Inherited
Molecular Function (MF)	peroxidase activity	0	Highly Informative	Direct
Molecular Function (MF)	heme binding	0	Highly Informative	Direct
Molecular Function (MF)	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge	0.04893	Highly Informative	Inherited
Cellular Component (CC)	intracellular organelle part	1	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.5943	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.05637	Least Informative	Inherited
Cellular Component (CC)	vacuole	5.201e-06	Informative	Direct
Cellular Component (CC)	external encapsulating structure	0	Informative	Direct
Cellular Component (CC)	plastid	0.01769	Informative	Inherited
Cellular Component (CC)	cell junction	0.01021	Informative	Inherited
Cellular Component (CC)	symplast	3.451e-06	Highly Informative	Direct
Cellular Component (CC)	cell-cell junction	0.001684	Highly Informative	Inherited
Cellular Component (CC)	cell wall	0.1308	Highly Informative	Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Oxidoreductases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on NADH or NADPH	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Acting on paired donors, with incorporation or red	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Miscellaneous (requires further characterization)	0	Informative	Direct
Enzyme Commission (EC)	Peroxidases	0.1679	Informative	Inherited
Enzyme Commission (EC)	With a oxygen as acceptor	0	Highly Informative	Direct
Enzyme Commission (EC)	Peroxidase	1.867e-15	Highly Informative	Direct

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)

	DO term	FDR (all)	SDDO level	Annotation (direct or inherited)
Disease Ontology (DO)	lung disease	0.0002503	Moderately Informative	Direct
Disease Ontology (DO)	endocrine system disease	0.0002506	Moderately Informative	Direct
Disease Ontology (DO)	disease by infectious agent	0.0006554	Moderately Informative	Direct
Disease Ontology (DO)	benign neoplasm	0.001401	Moderately Informative	Inherited
Disease Ontology (DO)	kidney disease	0.008925	Moderately Informative	Inherited
Disease Ontology (DO)	genetic disease	0.0343	Moderately Informative	Inherited
Disease Ontology (DO)	gastrointestinal system disease	0.2611	Moderately Informative	Inherited
Disease Ontology (DO)	nephritis	0.0005882	Informative	Direct
Disease Ontology (DO)	primary bacterial infectious disease	0.0009042	Informative	Direct
Disease Ontology (DO)	autosomal recessive disease	0.003723	Informative	Inherited
Disease Ontology (DO)	stomach disease	1.456e-05	Highly Informative	Direct
Disease Ontology (DO)	cystic fibrosis	0.0001924	Highly Informative	Direct

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details) Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)

	MP term	FDR (all)	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	immune system phenotype	0	Least Informative	Direct
Mammalian Phenotype (MP)	mortality/aging	0.1483	Least Informative	Inherited
Mammalian Phenotype (MP)	abnormal inflammatory response	0.02021	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal metabolism	9.678e-05	Informative	Direct
Mammalian Phenotype (MP)	autoimmune response	0.0008842	Informative	Direct
Mammalian Phenotype (MP)	increased sensitivity to induced morbidity/mortality	0.0009137	Informative	Direct
Mammalian Phenotype (MP)	increased physiological sensitivity to xenobiotic	0.0001976	Highly Informative	Direct
Mammalian Phenotype (MP)	decreased inflammatory response	0.0002585	Highly Informative	Direct
Mammalian Phenotype (MP)	altered susceptibility to autoimmune disorder	0.0004259	Highly Informative	Direct

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	growth variant	0	Least Informative	Direct
Worm Phenotype (WP)	larval development variant	0	Least Informative	Direct
Worm Phenotype (WP)	larval lethal	0	Moderately Informative	Direct
Worm Phenotype (WP)	molt variant	0.0006612	Highly Informative	Direct

Document: WP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	plant cell	1	Least Informative	Inherited
Plant ANatomical entity (PAN)	root epidermal cell	0.002753	Informative	Inherited
Plant ANatomical entity (PAN)	root hair cell	0.0004948	Highly Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Oxidoreductases	0	Least Informative	Direct
Enzyme Commission (EC)	Isomerases	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Acting on a peroxide as acceptor	0	Informative	Direct
Enzyme Commission (EC)	Acting on paired donors, with incorporation or reduction of molecular oxygen	1	Informative	Inherited
Enzyme Commission (EC)	Acting on NADH or NADPH	1	Informative	Inherited
Enzyme Commission (EC)	Intramolecular transferases (mutases)	1	Informative	Inherited
Enzyme Commission (EC)	Miscellaneous (requires further characterization)	0	Highly Informative	Direct
Enzyme Commission (EC)	With incorporation of two atoms of oxygen	0.01139	Highly Informative	Inherited
Enzyme Commission (EC)	Peroxidases	0.1698	Highly Informative	Inherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)

	DB term	FDR (all)	SDDB level	Annotation (direct or inherited)
Drugbank ATC_code (DB)	antiinfectives for systemic use	0.0005749	Moderately Informative	Direct
Drugbank ATC_code (DB)	antimycobacterials	4.412e-06	Informative	Direct

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Lipid metabolism	0.09131	Moderately Informative	Inherited
Biological process	Fatty acid metabolism	1.086e-06	Informative	Direct
Biological process	Lipid biosynthesis	0.005306	Informative	Inherited
Biological process	Prostaglandin biosynthesis	0	Highly Informative	Direct
Biological process	Thyroid hormones biosynthesis	0	Highly Informative	Direct
Biological process	Biological rhythms	3.443e-06	Highly Informative	Direct
Cellular component	Secreted	0	Moderately Informative	Direct
Cellular component	Endoplasmic reticulum	0.000816	Moderately Informative	Direct
Cellular component	Vacuole	8.688e-13	Informative	Direct
Cellular component	Microsome	2.393e-14	Highly Informative	Direct
Domain	Signal	0	Least Informative	Direct
Domain	EGF-like domain	5.714e-05	Informative	Direct
Domain	Sushi	0.0001296	Highly Informative	Direct
Molecular function	Metal-binding	0	Least Informative	Direct
Molecular function	Calcium	0	Moderately Informative	Direct
Molecular function	Iron	0	Moderately Informative	Direct
Molecular function	Heme	0	Informative	Direct
Molecular function	Potassium	1.211e-05	Informative	Direct
Post-translational modification	Oxidoreductase	0	Moderately Informative	Direct
Post-translational modification	Peroxidase	0	Highly Informative	Direct
Post-translational modification	Glycoprotein	0	Least Informative	Direct
Post-translational modification	Disulfide bond	0	Least Informative	Direct
Post-translational modification	Pyrrolidone carboxylic acid	0	Informative	Direct
Post-translational modification	S-nitrosylation	9.15e-10	Informative	Direct

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)

	UP term	FDR (all)	SDUP level	Annotation (direct or inherited)
UniPathway (UP)	lipid metabolism	2.572e-07	Least Informative	Direct
UniPathway (UP)	aromatic compound metabolism	0.03993	Least Informative	Inherited
UniPathway (UP)	fatty acid metabolism	4.459e-16	Moderately Informative	Direct
UniPathway (UP)	secondary metabolite metabolism	8.984e-14	Moderately Informative	Direct
UniPathway (UP)	hormone metabolism	0	Informative	Direct
UniPathway (UP)	thyroid hormone biosynthesis	0	Highly Informative	Direct
UniPathway (UP)	prostaglandin biosynthesis	0	Highly Informative	Direct

Document: UP annotation of SCOP domains

InterPro annotation

Cross references IPR010255 SSF48113 Protein matches

Abstract 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 animal peroxidases comprise a group of homologous proteins that differ markedly from the plant/fungal/bacterial peroxidases in primary, secondary and tertiary structure, but which share with them a common function. Animal peroxidases probably arose independently of the plant/fungal/bacterial peroxidase superfamily and most likely belong to a different gene family. The crystal structures of a number of these proteins show that the active sites of animal peroxidase and plant/fungal/bacterial peroxidases are remarkably similar [ PubMed 10403190].

InterPro database

PDBeMotif information about ligands, sequence and structure motifs

Cross references

PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 27 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a Heme-dependent peroxidases domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 27 hidden Markov models representing the Heme-dependent peroxidases superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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Heme-dependent peroxidases superfamily