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2 L-leucyl-tRNALeu
2 tRNALeu + cyclo(L-leucyl-L-leucyl)
L-leucyl-tRNALeu + L-leucyl-tRNALeu
tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
additional information
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2 L-leucyl-tRNALeu
2 tRNALeu + cyclo(L-leucyl-L-leucyl)
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2 L-leucyl-tRNALeu
2 tRNALeu + cyclo(L-leucyl-L-leucyl)
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2 L-leucyl-tRNALeu
2 tRNALeu + cyclo(L-leucyl-L-leucyl)
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2 L-leucyl-tRNALeu
2 tRNALeu + cyclo(L-leucyl-L-leucyl)
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L-leucyl-tRNALeu + L-leucyl-tRNALeu
tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
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L-leucyl-tRNALeu + L-leucyl-tRNALeu
tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
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L-leucyl-tRNALeu + L-leucyl-tRNALeu
tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
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L-leucyl-tRNALeu + L-leucyl-tRNALeu
tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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additional information
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the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue
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additional information
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the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue
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additional information
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the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue
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additional information
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the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides
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additional information
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides
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additional information
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enzyme AlbC uses aminoacyl-tRNAs to synthesize various cyclodipeptides, including the reactions of cyclo(L-tyrosyl-L-tyrosyl) synthase, EC 2.3.2.21, and cyclo(L-phenylalanyl-L-leucyl) synthase, EC 2.3.2.20
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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
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
evolution
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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
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evolution
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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
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evolution
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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
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evolution
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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
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evolution
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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
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evolution
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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
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evolution
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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
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evolution
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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
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metabolism
comparison of different CDPS-containing biosynthetic pathways, enzyme YvmC is involved in the pulcherrimin biosynthetic pathway, overview. In Bacillus subtilis, the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue. The yvmC gene is part of a two gene operon with cypX
metabolism
in Bacillus subtilis, the enzymes YvmC and CypX are involved in pulcherriminic acid biosynthesis. The cyclodipeptide synthase YvmC utilizes charged leucyl-tRNAs as substrate to catalyze the formation of cyclo-L-leucyl-L-leucyl (cLL). The cytochrome P450 CypX is implicated in the transformation of cLL into pulcherriminic acid. Pulcherriminic acid derived from cyclo-L-leucyl-L-leucyl is excreted and chelates free ferric ions to form the pulcherrimin. Analysis of mechanisms controlling the transcription of the yvmC-cypX operon, overview. The Bacillus subtilis YvmB MarR-like regulator is the major transcription factor controlling yvmC-cypX expression, involvement of YvmB as repressor in the control of yvm-CcypX expression. Expression of yvmB depends on iron availability. Genes yvmBA, yvmC-cypX and yvnB are identified for negative regulation and yisI for positive regulation. A 14-bp palindromic motif constitutes the YvmB binding site. YvmB might not control expression of yisI, whose encoding protein plays a negative role in the regulation of the sporulation initiation pathway. YvmB appears as an additional regulatory element into the cell's decision to grow or sporulate
metabolism
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in Bacillus subtilis, the enzymes YvmC and CypX are involved in pulcherriminic acid biosynthesis. The cyclodipeptide synthase YvmC utilizes charged leucyl-tRNAs as substrate to catalyze the formation of cyclo-L-leucyl-L-leucyl (cLL). The cytochrome P450 CypX is implicated in the transformation of cLL into pulcherriminic acid. Pulcherriminic acid derived from cyclo-L-leucyl-L-leucyl is excreted and chelates free ferric ions to form the pulcherrimin. Analysis of mechanisms controlling the transcription of the yvmC-cypX operon, overview. The Bacillus subtilis YvmB MarR-like regulator is the major transcription factor controlling yvmC-cypX expression, involvement of YvmB as repressor in the control of yvm-CcypX expression. Expression of yvmB depends on iron availability. Genes yvmBA, yvmC-cypX and yvnB are identified for negative regulation and yisI for positive regulation. A 14-bp palindromic motif constitutes the YvmB binding site. YvmB might not control expression of yisI, whose encoding protein plays a negative role in the regulation of the sporulation initiation pathway. YvmB appears as an additional regulatory element into the cell's decision to grow or sporulate
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metabolism
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comparison of different CDPS-containing biosynthetic pathways, enzyme YvmC is involved in the pulcherrimin biosynthetic pathway, overview. In Bacillus subtilis, the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue. The yvmC gene is part of a two gene operon with cypX
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metabolism
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comparison of different CDPS-containing biosynthetic pathways, enzyme YvmC is involved in the pulcherrimin biosynthetic pathway, overview. In Bacillus subtilis, the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue. The yvmC gene is part of a two gene operon with cypX
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metabolism
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comparison of different CDPS-containing biosynthetic pathways, enzyme YvmC is involved in the pulcherrimin biosynthetic pathway, overview. In Bacillus subtilis, the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue. The yvmC gene is part of a two gene operon with cypX
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physiological function
cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview
physiological function
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cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview
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physiological function
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cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview
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physiological function
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cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview
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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
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
additional information
the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS
additional information
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the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS
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additional information
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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
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additional information
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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
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additional information
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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
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additional information
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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
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additional information
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the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS
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additional information
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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
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additional information
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the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS
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additional information
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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
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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
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additional information
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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
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Gondry, M.; Sauguet, L.; Belin, P.; Thai, R.; Amouroux, R.; Tellier, C.; Tuphile, K.; Jacquet, M.; Braud, S.; Courcon, M.; Masson, C.; Dubois, S.; Lautru, S.; Lecoq, A.; Hashimoto, S.; Genet, R.; Pernodet, J.L.
Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes
Nat. Chem. Biol.
5
414-420
2009
Bacillus subtilis, Streptomyces noursei (Q8GED7)
brenda
Bonnefond, L.; Arai, T.; Sakaguchi, Y.; Suzuki, T.; Ishitani, R.; Nureki, O.
Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog
Proc. Natl. Acad. Sci. USA
108
3912-3917
2011
Bacillus licheniformis (Q65EX3), Bacillus licheniformis ATCC 14580 (Q65EX3)
brenda
Randazzo, P.; Aubert-Frambourg, A.; Guillot, A.; Auger, S.
The MarR-like protein PchR (YvmB) regulates expression of genes involved in pulcherriminic acid biosynthesis and in the initiation of sporulation in Bacillus subtilis
BMC Microbiol.
16
190
2016
Bacillus subtilis (O34351), Bacillus subtilis 168 (O34351)
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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
J. Struct. Biol.
203
17-26
2018
Staphylococcus haemolyticus (Q4L2X9), Bacillus licheniformis (Q65EX3), Bacillus licheniformis NCIMB 9375 (Q65EX3), Bacillus licheniformis Gibson 46 (Q65EX3), Bacillus licheniformis JCM 2505 (Q65EX3), Bacillus licheniformis NRRL NRS-1264 (Q65EX3), Bacillus licheniformis NBRC 12200 (Q65EX3), Bacillus licheniformis ATCC 14580 (Q65EX3), Bacillus licheniformis DSM 13 (Q65EX3), Staphylococcus haemolyticus JCSC1435 (Q4L2X9)
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Borgman, P.; Lopez, R.; Lane, A.
The expanding spectrum of diketopiperazine natural product biosynthetic pathways containing cyclodipeptide synthases
Org. Biomol. Chem.
17
2305-2314
2019
Bacillus spizizenii (E0U3N2), Bacillus spizizenii W23 (E0U3N2), Bacillus spizizenii NRRL B-14472 (E0U3N2), Bacillus spizizenii ATCC 23059 (E0U3N2)
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