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Literature summary extracted from
- Ferroxidase-mediated iron oxide biomineralization novel pathways to multifunctional nanoparticles (2016), Trends Biochem. Sci., 41, 190-203 .
Application
| EC Number | Application | Comment | Organism |
|---|---|---|---|
| 1.16.3.1 | biotechnology | compartmentalized iron oxide biomineralization by the enzyme yields uniform nanoparticles strictly determined by the sizes of the compartments, allowing customization for highly diverse nanotechnological applications | Microbacterium arborescens |
| 1.16.3.1 | biotechnology | compartmentalized iron oxide biomineralization by the enzyme yields uniform nanoparticles strictly determined by the sizes of the compartments, allowing customization for highly diverse nanotechnological applications | Myxococcus xanthus |
| 1.16.3.1 | biotechnology | compartmentalized iron oxide biomineralization by the enzyme yields uniform nanoparticles strictly determined by the sizes of the compartments, allowing customization for highly diverse nanotechnological applications | Thermotoga maritima |
| 1.16.3.1 | biotechnology | compartmentalized iron oxide biomineralization by the enzyme yields uniform nanoparticles strictly determined by the sizes of the compartments, allowing customization for highly diverse nanotechnological applications | Halobacterium salinarum |
| 1.16.3.1 | biotechnology | compartmentalized iron oxide biomineralization by the enzyme yields uniform nanoparticles strictly determined by the sizes of the compartments, allowing customization for highly diverse nanotechnological applications | Vibrio cholerae |
| 1.16.3.1 | biotechnology | compartmentalized iron oxide biomineralization by the enzyme yields uniform nanoparticles strictly determined by the sizes of the compartments, allowing customization for highly diverse nanotechnological applications | Streptomyces coelicolor |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 1.16.3.1 | crystal structure analysis, PDB ID 1TJO | Halobacterium salinarum |
| 1.16.3.1 | crystal structure analysis, PDB ID 3DKT | Thermotoga maritima |
| 1.16.3.1 | crystal structure analysis, PDB ID 4PT2 | Myxococcus xanthus |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Microbacterium arborescens | - |
4 Fe(III) + 2 H2O | - |
? |  |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Myxococcus xanthus | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Thermotoga maritima | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Halobacterium salinarum | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Vibrio cholerae | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Streptomyces coelicolor | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Vibrio cholerae B33 | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Myxococcus xanthus DK 1622 | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145 | - |
4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | Halobacterium salinarum ATCC 29341 | - |
4 Fe(III) + 2 H2O | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 1.16.3.1 | Halobacterium salinarum | B0R7W1 | - |
- |
| 1.16.3.1 | Halobacterium salinarum ATCC 29341 | B0R7W1 | - |
- |
| 1.16.3.1 | Microbacterium arborescens | - |
- |
- |
| 1.16.3.1 | Myxococcus xanthus | Q1D6H4 | - |
- |
| 1.16.3.1 | Myxococcus xanthus DK 1622 | Q1D6H4 | - |
- |
| 1.16.3.1 | Streptomyces coelicolor | Q9R408 | - |
- |
| 1.16.3.1 | Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145 | Q9R408 | - |
- |
| 1.16.3.1 | Thermotoga maritima | Q9WZP2 | - |
- |
| 1.16.3.1 | Vibrio cholerae | A0A0H3Q5A5 | - |
- |
| 1.16.3.1 | Vibrio cholerae B33 | A0A0H3Q5A5 | - |
- |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Microbacterium arborescens | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Myxococcus xanthus | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Thermotoga maritima | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Halobacterium salinarum | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Vibrio cholerae | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Streptomyces coelicolor | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Vibrio cholerae B33 | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Myxococcus xanthus DK 1622 | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145 | 4 Fe(III) + 2 H2O | - |
? | |
| 1.16.3.1 | 4 Fe(II) + 4 H+ + O2 | - |
Halobacterium salinarum ATCC 29341 | 4 Fe(III) + 2 H2O | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 1.16.3.1 | dimer | dodecamer or dimer, structure analysis, overview | Halobacterium salinarum |
| 1.16.3.1 | dodecamer | - |
Streptomyces coelicolor |
| 1.16.3.1 | dodecamer | structure analysis, overview | Microbacterium arborescens |
| 1.16.3.1 | dodecamer | structure analysis, overview | Vibrio cholerae |
| 1.16.3.1 | dodecamer | dodecamer or dimer, structure analysis, overview | Halobacterium salinarum |
| 1.16.3.1 | More | structure analysis, overview | Myxococcus xanthus |
| 1.16.3.1 | More | structure analysis, overview | Thermotoga maritima |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 1.16.3.1 | bacterial ferroxidase | - |
Microbacterium arborescens |
| 1.16.3.1 | bacterial ferroxidase | - |
Myxococcus xanthus |
| 1.16.3.1 | bacterial ferroxidase | - |
Thermotoga maritima |
| 1.16.3.1 | bacterial ferroxidase | - |
Halobacterium salinarum |
| 1.16.3.1 | bacterial ferroxidase | - |
Vibrio cholerae |
| 1.16.3.1 | bacterial ferroxidase | - |
Streptomyces coelicolor |
| 1.16.3.1 | DspA | - |
Halobacterium salinarum |
| 1.16.3.1 | DspA | - |
Streptomyces coelicolor |
| 1.16.3.1 | EncA | - |
Myxococcus xanthus |
| 1.16.3.1 | encapsulin | - |
Thermotoga maritima |
| 1.16.3.1 | encapsulin A | - |
Myxococcus xanthus |
| 1.16.3.1 | ferritin | - |
Halobacterium salinarum |
| 1.16.3.1 | ferritin | - |
Streptomyces coelicolor |
| 1.16.3.1 | MaDps | - |
Microbacterium arborescens |
| 1.16.3.1 | non-specific DNA-binding protein Dps/ferroxidase | UniProt | Vibrio cholerae |
| 1.16.3.1 | VcDps | - |
Vibrio cholerae |
| 1.16.3.1 | VCE_000308 | gene name, UniProt | Vibrio cholerae |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 1.16.3.1 | additional information | Dps protein structure and mechanism for ferroxidase-mediated biomineralization, overview | Microbacterium arborescens |
| 1.16.3.1 | additional information | Dps protein structure and mechanism for ferroxidase-mediated biomineralization, overview. Vibrio cholerae Dps (VcDps) and DpsA representing type I and II channels | Vibrio cholerae |
| 1.16.3.1 | additional information | encapsulin A is comprising 180 virus-like structural proteins with an outer diameter of 32 nm. Mechanism for ferroxidase-mediated biomineralization, overview | Myxococcus xanthus |
| 1.16.3.1 | additional information | encapsulin is comprising 60 virus-like structural proteins with an outer diameter of 24 nm. Mechanism for ferroxidase-mediated biomineralization, overview | Thermotoga maritima |
| 1.16.3.1 | additional information | in the dodecameric Dps, translocation position T3 is located at the channel exit where conserved Asp residues narrow the pore diameter significantly, forming a scaffold for tethering ions at the inner wall of the protein. After crossing the constriction zone, three ferroxidase centers are located about 20 A apart and iron can move along negatively charged residues at the inner wall towards the ferroxidase center with high-affinity binding. Mechanism for ferroxidase-mediated biomineralization, overview | Streptomyces coelicolor |
| 1.16.3.1 | additional information | the dodecameric Dps protein with an outer particle radius of 8 nm and a storage capacity of about 500 iron atoms. Ferritin can be assembled using six tetramers per cubic face, while Dps complexes are formed through the assembly of six protein dimers on each plane of the cube. Mechanism for ferroxidase-mediated biomineralization, overview | Halobacterium salinarum |
| 1.16.3.1 | physiological function | ferroxidase-mediated iron oxide biomineralization. The formation of iron-oxo particles in all these compartments requires a series of steps including recruitment of iron, translocation, oxidation, nucleation, and storage, that are mediated by ferroxidase centers. Compartmentalized iron oxide biomineralization yields uniform nanoparticles strictly determined by the sizes of the compartments. Dps, ferritin, and encapsulin all form protein-coated minerals of variable small sizes with similar iron oxide composition | Microbacterium arborescens |
| 1.16.3.1 | physiological function | ferroxidase-mediated iron oxide biomineralization. The formation of iron-oxo particles in all these compartments requires a series of steps including recruitment of iron, translocation, oxidation, nucleation, and storage, that are mediated by ferroxidase centers. Compartmentalized iron oxide biomineralization yields uniform nanoparticles strictly determined by the sizes of the compartments. Dps, ferritin, and encapsulin all form protein-coated minerals of variable small sizes with similar iron oxide composition | Myxococcus xanthus |
| 1.16.3.1 | physiological function | ferroxidase-mediated iron oxide biomineralization. The formation of iron-oxo particles in all these compartments requires a series of steps including recruitment of iron, translocation, oxidation, nucleation, and storage, that are mediated by ferroxidase centers. Compartmentalized iron oxide biomineralization yields uniform nanoparticles strictly determined by the sizes of the compartments. Dps, ferritin, and encapsulin all form protein-coated minerals of variable small sizes with similar iron oxide composition | Thermotoga maritima |
| 1.16.3.1 | physiological function | ferroxidase-mediated iron oxide biomineralization. The formation of iron-oxo particles in all these compartments requires a series of steps including recruitment of iron, translocation, oxidation, nucleation, and storage, that are mediated by ferroxidase centers. Compartmentalized iron oxide biomineralization yields uniform nanoparticles strictly determined by the sizes of the compartments. Dps, ferritin, and encapsulin all form protein-coated minerals of variable small sizes with similar iron oxide composition | Halobacterium salinarum |
| 1.16.3.1 | physiological function | ferroxidase-mediated iron oxide biomineralization. The formation of iron-oxo particles in all these compartments requires a series of steps including recruitment of iron, translocation, oxidation, nucleation, and storage, that are mediated by ferroxidase centers. Compartmentalized iron oxide biomineralization yields uniform nanoparticles strictly determined by the sizes of the compartments. Dps, ferritin, and encapsulin all form protein-coated minerals of variable small sizes with similar iron oxide composition | Vibrio cholerae |
| 1.16.3.1 | physiological function | ferroxidase-mediated iron oxide biomineralization. The formation of iron-oxo particles in all these compartments requires a series of steps including recruitment of iron, translocation, oxidation, nucleation, and storage, that are mediated by ferroxidase centers. Compartmentalized iron oxide biomineralization yields uniform nanoparticles strictly determined by the sizes of the compartments. Dps, ferritin, and encapsulin all form protein-coated minerals of variable small sizes with similar iron oxide composition | Streptomyces coelicolor |
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