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Literature summary for 1.11.1.B7 extracted from
- Secreted heme peroxidase from Dictyostelium discoideum insights into catalysis, structure, and biological role (2018), J. Biol. Chem., 293, 1330-1345 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene poxA, recombinant expression of N-terminally His-tagged enzyme in Pichia pastoris strain BG11 the enzyme is secreted, recombinant expression of GFP-tagged enzyme in Dictyostelium discoideum cells | Dictyostelium discoideum |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| analysis of the enzyme crystal structure determined at 2.5 A resolution, molecular replacement | Dictyostelium discoideum |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | construction of DELTADdpoxA mutant cells. The mutant has significant deficiencies in keeping the slug and the sori sterile upon cell development | Dictyostelium discoideum |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | pre-steady-state kinetics and stopped-flow kinetic analysis, overview | Dictyostelium discoideum |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| endosome | recycling | Dictyostelium discoideum | 5768 | - |
| extracellular | - |
Dictyostelium discoideum | - |
- |
| Golgi apparatus | - |
Dictyostelium discoideum | 5794 | - |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 60700 | - |
about, sequence calculation | Dictyostelium discoideum |
| 63400 | - |
gel filtration | Dictyostelium discoideum |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Dictyostelium discoideum | Q6TMK4 | - |
- |
Posttranslational Modification
| Posttranslational Modification | Comment | Organism |
|---|---|---|
| glycoprotein | the secreted glycosylated peroxidase has three N-glycosylation sites at positions Asn62, Asn131, and Asn338. The overall and heme cavity architecture are not affected at pH 5.0 and pH 9.0 by deglycosylation through Endo Hf glucosidase | Dictyostelium discoideum |
| additional information | autocatalytic posttranslational modification of the heme group without requirement for hydrogen peroxide | Dictyostelium discoideum |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant extracellular N-terminally His-tagged enzyme from Pichia pastoris strain BG11 by ammonium sulfate fractionation and nickel affinity chromatography | Dictyostelium discoideum |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| additional information | expression of DdPoxA is upregulated at late developmental stages, starting approximately from 12 h after initiation of starvation | Dictyostelium discoideum | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| DdPoxA + bromide + H2O2 | DdPoxA compound I is the redox intermediate formed by the Fe(III) form with H2O2 | Dictyostelium discoideum | ? | - |
? |  |
| DdPoxA + chloride + H2O2 | DdPoxA compound I is the redox intermediate formed by the Fe(III) form with H2O2 | Dictyostelium discoideum | ? | - |
? | |
| DdPoxA + cyanide + H2O2 | DdPoxA compound I is the redox intermediate formed by the Fe(III) form with H2O2, formation of the DdPoxA-cyanide low spin complex | Dictyostelium discoideum | ? | - |
? | |
| DdPoxA + iodide + H2O2 | DdPoxA compound I is the redox intermediate formed by the Fe(III) form with H2O2 | Dictyostelium discoideum | ? | - |
? | |
| DdPoxA + thiocyanate + H2O2 | DdPoxA compound I is the redox intermediate formed by the Fe(III) form with H2O2 | Dictyostelium discoideum | ? | - |
? | |
| additional information | reaction of ferric DdPoxA with cyanide and H2O2 and reaction of compound I with bromide, stopped-flow measurements. DdPoxA compound I is an efficient oxidant of iodide and thiocyanate | Dictyostelium discoideum | ? | - |
- |
|
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer | 1 * 60700, about, sequence calculation | Dictyostelium discoideum |
| More | the enzyme structure shows the overall largely alpha-helical structural organization of DdPoxA. Only three small antiparallel beta-strands (residues Phe43-Pro46, Ala141-Glu143, and Tyr160-Asn164) are present. The protein is composed of 21 alpha-helices of varying length. The central core of the molecule consists of five long alpha-helices (H2, H6, H7, H8, and H13) with the covalently attached heme | Dictyostelium discoideum |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| DdPoxA | - |
Dictyostelium discoideum |
| heme peroxidase | - |
Dictyostelium discoideum |
| More | cf. EC 1.11.1.7 | Dictyostelium discoideum |
| peroxinectin A | UniProt | Dictyostelium discoideum |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 25 | - |
assay at | Dictyostelium discoideum |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 59.6 | - |
recombinant deglycosylated DdPoxA at pH 7.0 shows a mid-point transition of 59.6°C in the far-UV at 208 nm reflecting unfolding of the secondary structure | Dictyostelium discoideum |
| 62 | - |
recombinant glycosylated DdPoxA at pH 7.0 shows a mid-point transition of 62°C in the far-UV at 208 nm reflecting unfolding of the secondary structure | Dictyostelium discoideum |
| 71.1 | 80.4 | recombinant ferric glycosylated DdPoxA shows two independent unfolding events with Tm values of 71.1°C and 80.4°C, respectively, at pH 7.0. The thermal stability rapidly decreases at alkaline pH, whereas stability is retained in the acidic region until pH 5.0 | Dictyostelium discoideum |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7 | - |
assay at | Dictyostelium discoideum |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| heme | DdPoxA displays high structural similarity to mammalian peroxidases but unusual post-translational heme modification | Dictyostelium discoideum | |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Dictyostelium discoideum | expression of DdPoxA is upregulated at late developmental stages, starting approximately from 12 h after initiation of starvation | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | DdPoxA is a member of the peroxidase-cyclooxygenase superfamily, family 6. Phylogenetic reconstruction of the main evolutionary lines of the mammalian heme peroxidases such as lactoperoxidase or myeloperoxidase reveals the presence of other bacterial and early eukaryotic representatives within family 6 of the peroxidase-cyclooxygenase superfamily | Dictyostelium discoideum |
| malfunction | the DELTADdpoxA mutant has significant deficiencies in keeping the slug and the sori sterile upon cell development | Dictyostelium discoideum |
| additional information | active site architecture analysis and comparison, e.g. to lactoperoxidase (LPO). DdPoxA has only one covalent link between the 1-methyl substituent of the prosthetic group and Glu236 because the DdPoxA residue corresponding to Asp-225 of LPO is an isoleucine. The important catalytic residues on the distal heme site (His101, Gln97, and Arg233) are fully conserved, including Glu236 that forms an ester bond with the 1-methyl substituent of the heme porphyrin ring | Dictyostelium discoideum |
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Release 2023.1 (January 2023)
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