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Literature summary for 2.3.2.20 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 | Streptomyces noursei |
| 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 | Nocardia brasiliensis |
| 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 | Rickettsiella grylli |
| 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 | Fluoribacter dumoffii |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene albC, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha | Streptomyces noursei |
| gene NCTC11370_02388, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha | Fluoribacter dumoffii |
| gene O3I_025450, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha | Nocardia brasiliensis |
| gene RICGR_0139, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha | Rickettsiella grylli |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant enzyme, crystallization from 11% PEG 3350, 0.1 M HEPES, pH 7.5, and 0.2 M L-Pro, X-ray difffraction structure determination and analysis at 3.06 A resolution | Fluoribacter dumoffii |
| purified recombinant enzyme, crystallization from 15.2% PEG 3350, 0.1 M potassium fluoride, X-ray difffraction structure determination and analysis at 1.99 A resolution | Rickettsiella grylli |
| purified recombinant enzyme, crystallization from 22% PEG 3350, 0.2 M tri-ammonium citrate, pH 7.0, X-ray difffraction structure determination and analysis at 3.18 A resolution | Nocardia brasiliensis |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Fluoribacter dumoffii | A0A377GCR9 | - |
- |
| Nocardia brasiliensis | K0F6G5 | - |
- |
| Nocardia brasiliensis ATCC 700358 | K0F6G5 | - |
- |
| Rickettsiella grylli | A8PKE0 | - |
- |
| Rickettsiella grylli ATCC 700358 | A8PKE0 | - |
- |
| Streptomyces noursei | Q8GED7 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Escherichia coli strain BL21AI | Streptomyces noursei |
| recombinant enzyme from Escherichia coli strain BL21AI | Nocardia brasiliensis |
| recombinant enzyme from Escherichia coli strain BL21AI | Rickettsiella grylli |
| recombinant enzyme from Escherichia coli strain BL21AI | Fluoribacter dumoffii |
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 | Streptomyces noursei | ? | - |
- |
 |
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Nocardia brasiliensis | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Rickettsiella grylli | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Fluoribacter dumoffii | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Nocardia brasiliensis ATCC 700358 | ? | - |
- |
|
| additional information | cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides | Rickettsiella grylli ATCC 700358 | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| AlbC | - |
Streptomyces noursei |
| CDPS | - |
Streptomyces noursei |
| CDPS | - |
Nocardia brasiliensis |
| CDPS | - |
Rickettsiella grylli |
| CDPS | - |
Fluoribacter dumoffii |
| CDPS39 | - |
Nocardia brasiliensis |
| cyclodipeptide synthase | - |
Streptomyces noursei |
| cyclodipeptide synthase | - |
Nocardia brasiliensis |
| cyclodipeptide synthase | - |
Rickettsiella grylli |
| cyclodipeptide synthase | - |
Fluoribacter dumoffii |
| Fdum-CDPS | - |
Fluoribacter dumoffii |
| Nbra-CDPS | - |
Nocardia brasiliensis |
| NCTC11370_02388 | - |
Fluoribacter dumoffii |
| O3I_025450 | - |
Nocardia brasiliensis |
| Rgry-CDPS | - |
Rickettsiella grylli |
| RICGR_0139 | - |
Rickettsiella grylli |
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 Fluoribacter dumoffii belongs to the XYP subfamily | Fluoribacter dumoffii |
| 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 Nocardia brasiliensis belongs to the XYP subfamily | Nocardia brasiliensis |
| 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 Rickettsiella grylli belongs to the XYP subfamily | Rickettsiella grylli |
| 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 Streptomyces noursei belongs to the NYH subfamily | Streptomyces noursei |
| 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. 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 | Streptomyces noursei |
| 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 | Nocardia brasiliensis |
| 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 | Rickettsiella grylli |
| 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 | Fluoribacter dumoffii |
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