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Literature summary for 2.3.2.22 extracted from
- Structural basis for partition of the cyclodipeptide synthases into two subfamilies (2018), J. Struct. Biol., 203, 17-26 .
Application
| Application | Comment | Organism |
|---|---|---|
| synthesis | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines | Bacillus licheniformis |
| synthesis | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines | Staphylococcus haemolyticus |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene pSHaeC06, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha | Staphylococcus haemolyticus |
| gene yvmC, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha | Bacillus licheniformis |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant enzyme, crystallization from 30% PEG 4000, 0.1 M Tris-HCl, pH 8.5, and 0.2 M lithium sulfate monohydrate, X-ray diffraction structure determination and analysis at 2.99 A resolution | Staphylococcus haemolyticus |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus licheniformis | Q65EX3 | - |
- |
| Bacillus licheniformis ATCC 14580 | Q65EX3 | - |
- |
| Bacillus licheniformis DSM 13 | Q65EX3 | - |
- |
| Bacillus licheniformis Gibson 46 | Q65EX3 | - |
- |
| Bacillus licheniformis JCM 2505 | Q65EX3 | - |
- |
| Bacillus licheniformis NBRC 12200 | Q65EX3 | - |
- |
| Bacillus licheniformis NCIMB 9375 | Q65EX3 | - |
- |
| Bacillus licheniformis NRRL NRS-1264 | Q65EX3 | - |
- |
| Staphylococcus haemolyticus | Q4L2X9 | - |
- |
| Staphylococcus haemolyticus JCSC1435 | Q4L2X9 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Escherichia coli strain BL21AI | Bacillus licheniformis |
| recombinant enzyme from Escherichia coli strain BL21AI | Staphylococcus haemolyticus |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Staphylococcus haemolyticus | ? | - |
- |
 |
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis NCIMB 9375 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis Gibson 46 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis JCM 2505 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis NRRL NRS-1264 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis NBRC 12200 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis ATCC 14580 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview | Bacillus licheniformis DSM 13 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Staphylococcus haemolyticus JCSC1435 | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| CDPS | - |
Bacillus licheniformis |
| CDPS | - |
Staphylococcus haemolyticus |
| cyclo(L-leucyl-L-leucyl) synthase | - |
Bacillus licheniformis |
| cyclo(L-leucyl-L-leucyl) synthase | - |
Staphylococcus haemolyticus |
| cyclodipeptide synthase | - |
Bacillus licheniformis |
| cyclodipeptide synthase | - |
Staphylococcus haemolyticus |
| pSHaeC06 | - |
Staphylococcus haemolyticus |
| Shae-CDPS | - |
Staphylococcus haemolyticus |
| YvmC | - |
Bacillus licheniformis |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. Comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold. The XYP and NYH motifs correspond to two structural solutions to facilitate the reactivity of the catalytic serine residue. The CDPS from Bacillus licheniformis belongs to the NYH subfamily | Bacillus licheniformis |
| evolution | CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. Comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold. The XYP and NYH motifs correspond to two structural solutions to facilitate the reactivity of the catalytic serine residue. The CDPS from Staphylococcus haemolyticus belongs to the TYH subfamily | Staphylococcus haemolyticus |
| additional information | CDPSs structure comparisons, comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold, overview. The CDPS adopts a common architecture with a monomer built around a Rossmann fold domain that displays structural similarity to the catalytic domain of the two class Ic aminoacyl-tRNA synthetases (aaRSs), TyrRS and TrpRS. It contains a deep surface-accessible pocket P1, the location of which corresponds to that of the aminoacyl-binding pocket of the two aaRSs. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. Despite these differences, the key catalytic residues (S37, Y202, Y178 and E182, AlbC numbering) are conserved in all CDPSs and have a same location in the catalytic centre of the enzymes. Residues belonging to the signature sequences play parallel roles in the two subfamilies, contributing to the positioning of the catalytic serine and of the crucial Y202 residue. The mode of action of the signature residues however differs, with a more complex network of hydrogen bonds in NYH enzymes. Notably, the signature residues are located in the two catalytic loops at the switch point between the two halves of the Rossmann fold | Bacillus licheniformis |
| additional information | CDPSs structure comparisons, comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold, overview. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. Despite these differences, the key catalytic residues (S37, Y202, Y178 and E182, AlbC numbering) are conserved in all CDPSs and have a same location in the catalytic centre of the enzymes. Residues belonging to the signature sequences play parallel roles in the two subfamilies, contributing to the positioning of the catalytic serine and of the crucial Y202 residue. The mode of action of the signature residues however differs, with a more complex network of hydrogen bonds in NYH enzymes. Notably, the signature residues are located in the two catalytic loops at the switch point between the two halves of the Rossmann fold | Staphylococcus haemolyticus |
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Release 2023.1 (January 2023)
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