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Literature summary extracted from

  • Bourgeois, G.; Seguin, J.; Babin, M.; Belin, P.; Moutiez, M.; Mechulam, Y.; Gondry, M.; Schmitt, E.
    Structural basis for partition of the cyclodipeptide synthases into two subfamilies (2018), J. Struct. Biol., 203, 17-26 .
    View publication on PubMed

Application

EC Number Application Comment Organism
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.21 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 Mycobacterium tuberculosis
2.3.2.22 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
2.3.2.22 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)

EC Number Cloned (Comment) Organism
2.3.2.20 gene albC, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Streptomyces noursei
2.3.2.20 gene NCTC11370_02388, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Fluoribacter dumoffii
2.3.2.20 gene O3I_025450, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Nocardia brasiliensis
2.3.2.20 gene RICGR_0139, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Rickettsiella grylli
2.3.2.21 gene Rv2275, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Mycobacterium tuberculosis
2.3.2.22 gene pSHaeC06, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Staphylococcus haemolyticus
2.3.2.22 gene yvmC, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha Bacillus licheniformis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.22 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

EC Number Organism UniProt Comment Textmining
2.3.2.20 Fluoribacter dumoffii A0A377GCR9
-
-
2.3.2.20 Nocardia brasiliensis K0F6G5
-
-
2.3.2.20 Nocardia brasiliensis ATCC 700358 K0F6G5
-
-
2.3.2.20 Rickettsiella grylli A8PKE0
-
-
2.3.2.20 Rickettsiella grylli ATCC 700358 A8PKE0
-
-
2.3.2.20 Streptomyces noursei Q8GED7
-
-
2.3.2.21 Mycobacterium tuberculosis P9WPF9
-
-
2.3.2.21 Mycobacterium tuberculosis ATCC 25618 P9WPF9
-
-
2.3.2.21 Mycobacterium tuberculosis H37Rv P9WPF9
-
-
2.3.2.22 Bacillus licheniformis Q65EX3
-
-
2.3.2.22 Bacillus licheniformis ATCC 14580 Q65EX3
-
-
2.3.2.22 Bacillus licheniformis DSM 13 Q65EX3
-
-
2.3.2.22 Bacillus licheniformis Gibson 46 Q65EX3
-
-
2.3.2.22 Bacillus licheniformis JCM 2505 Q65EX3
-
-
2.3.2.22 Bacillus licheniformis NBRC 12200 Q65EX3
-
-
2.3.2.22 Bacillus licheniformis NCIMB 9375 Q65EX3
-
-
2.3.2.22 Bacillus licheniformis NRRL NRS-1264 Q65EX3
-
-
2.3.2.22 Staphylococcus haemolyticus Q4L2X9
-
-
2.3.2.22 Staphylococcus haemolyticus JCSC1435 Q4L2X9
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.3.2.20 recombinant enzyme from Escherichia coli strain BL21AI Streptomyces noursei
2.3.2.20 recombinant enzyme from Escherichia coli strain BL21AI Nocardia brasiliensis
2.3.2.20 recombinant enzyme from Escherichia coli strain BL21AI Rickettsiella grylli
2.3.2.20 recombinant enzyme from Escherichia coli strain BL21AI Fluoribacter dumoffii
2.3.2.21 recombinant enzyme from Escherichia coli strain BL21AI Mycobacterium tuberculosis
2.3.2.22 recombinant enzyme from Escherichia coli strain BL21AI Bacillus licheniformis
2.3.2.22 recombinant enzyme from Escherichia coli strain BL21AI Staphylococcus haemolyticus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.2.20 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Streptomyces noursei ?
-
-
2.3.2.20 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Nocardia brasiliensis ?
-
-
2.3.2.20 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Rickettsiella grylli ?
-
-
2.3.2.20 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Fluoribacter dumoffii ?
-
-
2.3.2.20 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Nocardia brasiliensis ATCC 700358 ?
-
-
2.3.2.20 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Rickettsiella grylli ATCC 700358 ?
-
-
2.3.2.21 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview Mycobacterium tuberculosis ?
-
-
2.3.2.21 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview Mycobacterium tuberculosis H37Rv ?
-
-
2.3.2.21 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview Mycobacterium tuberculosis ATCC 25618 ?
-
-
2.3.2.22 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Staphylococcus haemolyticus ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 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 ?
-
-
2.3.2.22 additional information cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides Staphylococcus haemolyticus JCSC1435 ?
-
-

Synonyms

EC Number Synonyms Comment Organism
2.3.2.20 AlbC
-
 Streptomyces noursei
2.3.2.20 CDPS
-
 Streptomyces noursei
2.3.2.20 CDPS
-
 Nocardia brasiliensis
2.3.2.20 CDPS
-
 Rickettsiella grylli
2.3.2.20 CDPS
-
 Fluoribacter dumoffii
2.3.2.20 CDPS39
-
 Nocardia brasiliensis
2.3.2.20 cyclodipeptide synthase
-
 Streptomyces noursei
2.3.2.20 cyclodipeptide synthase
-
 Nocardia brasiliensis
2.3.2.20 cyclodipeptide synthase
-
 Rickettsiella grylli
2.3.2.20 cyclodipeptide synthase
-
 Fluoribacter dumoffii
2.3.2.20 Fdum-CDPS
-
 Fluoribacter dumoffii
2.3.2.20 Nbra-CDPS
-
 Nocardia brasiliensis
2.3.2.20 NCTC11370_02388
-
 Fluoribacter dumoffii
2.3.2.20 O3I_025450
-
 Nocardia brasiliensis
2.3.2.20 Rgry-CDPS
-
 Rickettsiella grylli
2.3.2.20 RICGR_0139
-
 Rickettsiella grylli
2.3.2.21 CDPS
-
 Mycobacterium tuberculosis
2.3.2.21 cyclo(L-tyrosyl-L-tyrosyl) synthase
-
 Mycobacterium tuberculosis
2.3.2.21 cyclodipeptide synthase
-
 Mycobacterium tuberculosis
2.3.2.21 Rv2275
-
 Mycobacterium tuberculosis
2.3.2.22 CDPS
-
 Bacillus licheniformis
2.3.2.22 CDPS
-
 Staphylococcus haemolyticus
2.3.2.22 cyclo(L-leucyl-L-leucyl) synthase
-
 Bacillus licheniformis
2.3.2.22 cyclo(L-leucyl-L-leucyl) synthase
-
 Staphylococcus haemolyticus
2.3.2.22 cyclodipeptide synthase
-
 Bacillus licheniformis
2.3.2.22 cyclodipeptide synthase
-
 Staphylococcus haemolyticus
2.3.2.22 pSHaeC06
-
 Staphylococcus haemolyticus
2.3.2.22 Shae-CDPS
-
 Staphylococcus haemolyticus
2.3.2.22 YvmC
-
 Bacillus licheniformis

General Information

EC Number General Information Comment Organism
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.20 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
2.3.2.21 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 Mycobacterium tuberculosis belongs to the NYH subfamily Mycobacterium tuberculosis
2.3.2.21 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. 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 Mycobacterium tuberculosis
2.3.2.22 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
2.3.2.22 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
2.3.2.22 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
2.3.2.22 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