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Literature summary extracted from
- Crystal structures and biochemical analyses of intermediate cleavage peptidase role of dynamics in enzymatic function (2019), FEBS Lett., 593, 443-454 .
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 3.4.11.9 | expression in Escherichia coli BL21(DE3). Full-length Icp55 construct can not be expressed in the soluble fraction. Two truncated versions, Icp55t1 with 42 amino acid N-terminal truncation and Icp55t2 with 57 amino acid N-terminal truncation, are successfully expressed in soluble forms. All activity assays for Icp55 are reported for Icp55t1 construct | Saccharomyces cerevisiae |
| 3.4.11.26 | - |
Saccharomyces cerevisiae |
| 3.4.11.26 | expression in Escherichia coli BL21(DE3). Full-length Icp55 construct can not be expressed in the soluble fraction. Two truncated versions, Icp55t1 with 42 amino acid N-terminal truncation and Icp55t2 with 57 amino acid N-terminal truncation, are successfully expressed in soluble forms. All activity assays for Icp55 are reported for Icp55t1 construct | Saccharomyces cerevisiae |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 3.4.11.9 | oil microbatch method | Saccharomyces cerevisiae |
| 3.4.11.26 | free enzyme and in complex with inhibitor apstatin. The enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, and not the monomer, is the active species with loop dynamics at the dimer interface playing an important role in activity | Saccharomyces cerevisiae |
| 3.4.11.26 | oil microbatch method | Saccharomyces cerevisiae |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 3.4.11.26 | Y284D | mutation of a conserved Tyr284 residue located at hinge helix that interacts with its counterpart across the dimer interface. Mutant is a monomer | Saccharomyces cerevisiae |
Inhibitors
| EC Number | Inhibitors | Comment | Organism | Structure |
|---|---|---|---|---|
| 3.4.11.9 | apstatin | - |
Saccharomyces cerevisiae |  |
| 3.4.11.9 | EDTA | - |
Saccharomyces cerevisiae | |
| 3.4.11.9 | Tyr-Ala-Ala | - |
Saccharomyces cerevisiae | |
| 3.4.11.26 | apstatin | crystal data in complex with apstatin | Saccharomyces cerevisiae | |
| 3.4.11.26 | EDTA | complete loss of activity | Saccharomyces cerevisiae | |
| 3.4.11.26 | Tyr-Ala-Ala | - |
Saccharomyces cerevisiae | |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 3.4.11.9 | 0.72 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.9 | 1.8 | - |
Tyr-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.9 | 2 | - |
Met-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 0.72 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 1.8 | - |
Tyr-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 2 | - |
Met-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 3.4.11.9 | Mn2+ | the activity of the enzyme depends critically on the presence of Mn2+. Reducing concentration of Mn2+ in reaction buffer from 1 mM to 0.006 mM reduces the activity of the enzyme by about 60%. Other divalent metal ions (Mg2+, Ca2+, Co2+, Ni2+ and Zn2+) fail to fully restore activity of the enzyme | Saccharomyces cerevisiae | |
| 3.4.11.26 | Mn2+ | reducing concentration of Mn2+ in reaction buffer from 1 mM to 6 microM reduces the activity of the enzyme by about 60% | Saccharomyces cerevisiae | |
| 3.4.11.26 | Mn2+ | the activity of the enzyme depends critically on the presence of Mn2+. Reducing concentration of Mn2+ in reaction buffer from 1 mM to 0.006 mM reduces the activity of the enzyme by about 60%. Other divalent metal ions (Mg2+, Ca2+, Co2+, Ni2+ and Zn2+) fail to fully restore activity of the enzyme | Saccharomyces cerevisiae | |
| 3.4.11.26 | additional information | not activating: Mg2+, Ca2+, Co2+, Ni2+, Zn2+ | Saccharomyces cerevisiae |
Molecular Weight [Da]
| EC Number | Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|---|
| 3.4.11.9 | 106000 | - |
dimer, gel filtration | Saccharomyces cerevisiae |
| 3.4.11.26 | 53000 | - |
and 106000, gel filtration, truncated variant lacking 42 N-terminal amino acids | Saccharomyces cerevisiae |
| 3.4.11.26 | 106000 | - |
dimer, gel filtration | Saccharomyces cerevisiae |
| 3.4.11.26 | 106000 | - |
and 53000, gel filtration, truncated variant lacking 42 N-terminal amino acids | Saccharomyces cerevisiae |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 3.4.11.9 | Saccharomyces cerevisiae | P40051 | - |
- |
| 3.4.11.9 | Saccharomyces cerevisiae ATCC 204508 | P40051 | - |
- |
| 3.4.11.26 | Saccharomyces cerevisiae | P40051 | - |
- |
| 3.4.11.26 | Saccharomyces cerevisiae ATCC 204508 | P40051 | - |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 3.4.11.9 | - |
Saccharomyces cerevisiae |
| 3.4.11.26 | - |
Saccharomyces cerevisiae |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.4.11.9 | Met-Pro-Ala + H2O | - |
Saccharomyces cerevisiae | Met + Pro-Ala | - |
? | |
| 3.4.11.9 | Met-Pro-Ala + H2O | - |
Saccharomyces cerevisiae ATCC 204508 | Met + Pro-Ala | - |
? | |
| 3.4.11.9 | additional information | the enzyme is active towards substrates with proline at P1' position (M-/-PA and Y-/-PA). Icp55 cleaves off bulky residues from N-termini of proteins. Active towards substrates Y-/-AA, Y-/-TA and Y-/-SA | Saccharomyces cerevisiae | ? | - |
? | |
| 3.4.11.9 | additional information | the enzyme is active towards substrates with proline at P1' position (M-/-PA and Y-/-PA). Icp55 cleaves off bulky residues from N-termini of proteins. Active towards substrates Y-/-AA, Y-/-TA and Y-/-SA | Saccharomyces cerevisiae ATCC 204508 | ? | - |
? | |
| 3.4.11.9 | Tyr-Ala-Ala + H2O | - |
Saccharomyces cerevisiae | Tyr + Ala-Ala | - |
? | |
| 3.4.11.9 | Tyr-Ala-Ala + H2O | - |
Saccharomyces cerevisiae ATCC 204508 | Tyr + Ala-Ala | - |
? | |
| 3.4.11.9 | Tyr-Pro-Ala + H2O | - |
Saccharomyces cerevisiae | Tyr + Pro-Ala | - |
? | |
| 3.4.11.9 | Tyr-Pro-Ala + H2O | - |
Saccharomyces cerevisiae ATCC 204508 | Tyr + Pro-Ala | - |
? | |
| 3.4.11.26 | Met-Pro-Ala + H2O | - |
Saccharomyces cerevisiae | Met + Pro-Ala | - |
? | |
| 3.4.11.26 | additional information | residue Tyr is preferred at P1 position. The enzyme additionally displays Xaa-Pro aminopeptidase activity in vitro | Saccharomyces cerevisiae | ? | - |
? | |
| 3.4.11.26 | additional information | the enzyme is active towards substrates with proline at P1' position (M-/-PA and Y-/-PA). Icp55 cleaves off bulky residues from N-termini of proteins. Active towards substrates Y-/-AA, Y-/-TA and Y-/-SA | Saccharomyces cerevisiae | ? | - |
? | |
| 3.4.11.26 | additional information | residue Tyr is preferred at P1 position. The enzyme additionally displays Xaa-Pro aminopeptidase activity in vitro | Saccharomyces cerevisiae ATCC 204508 | ? | - |
? | |
| 3.4.11.26 | Tyr-Ala-Ala + H2O | - |
Saccharomyces cerevisiae | Tyr + Ala-Ala | - |
? | |
| 3.4.11.26 | Tyr-Pro-Ala + H2O | - |
Saccharomyces cerevisiae | Tyr + Pro-Ala | - |
? | |
| 3.4.11.26 | Tyr-Ser-Ala + H2O | - |
Saccharomyces cerevisiae | Tyr + Ser-Ala | - |
? | |
| 3.4.11.26 | Tyr-Thr-Ala + H2O | - |
Saccharomyces cerevisiae | Tyr + Thr-Ala | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 3.4.11.9 | dimer | 2 * 52000, gel filtration, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme with loop dynamics at the dimer interface playing an important role in activity. Dynamics of Icp55 protein between two conformations of dimer are found to be important for activity of the enzyme | Saccharomyces cerevisiae |
| 3.4.11.9 | monomer | 1 * 52000, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme | Saccharomyces cerevisiae |
| 3.4.11.26 | dimer | 2 * 52000, gel filtration, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme with loop dynamics at the dimer interface playing an important role in activity. Dynamics of Icp55 protein between two conformations of dimer are found to be important for activity of the enzyme | Saccharomyces cerevisiae |
| 3.4.11.26 | monomer | 1 * 52000, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme | Saccharomyces cerevisiae |
| 3.4.11.26 | monomer | and dimer, 1 * 58000 and 2 * 58000, calculated from sequence | Saccharomyces cerevisiae |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 3.4.11.9 | Icp55 | - |
Saccharomyces cerevisiae |
| 3.4.11.26 | Icp55 | - |
Saccharomyces cerevisiae |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 3.4.11.9 | 40 | - |
assay at | Saccharomyces cerevisiae |
| 3.4.11.26 | 40 | - |
assay at | Saccharomyces cerevisiae |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 3.4.11.9 | 1.4 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.9 | 14 | - |
Tyr-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.9 | 25.7 | - |
Met-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 1.4 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 14 | - |
Tyr-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 25.7 | - |
Met-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 3.4.11.9 | 7.5 | - |
assay at | Saccharomyces cerevisiae |
| 3.4.11.26 | 7.5 | - |
assay at | Saccharomyces cerevisiae |
Ki Value [mM]
| EC Number | Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 3.4.11.9 | 5 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 5 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
kcat/KM [mM/s]
| EC Number | kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 3.4.11.9 | 1.94 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.9 | 7.78 | - |
Tyr-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.9 | 12.8 | - |
Met-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 1.94 | - |
Tyr-Ala-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 7.78 | - |
Tyr-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
| 3.4.11.26 | 12.8 | - |
Met-Pro-Ala | pH 7.5, 40°C | Saccharomyces cerevisiae | |
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