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Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis.

Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M - Nucleic Acids Res. (2011)

Bottom Line: These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs.AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which L-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine.These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.

View Article: PubMed Central - PubMed

Affiliation: CEA, IBITECS, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France.

ABSTRACT
Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which L-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.

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The reaction catalysed by CDPSs. CDPSs use activated amino acids, in the form of aa-tRNAs, as substrates to catalyse the formation of cyclodipeptides, also known as DKPs.
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Figure 1: The reaction catalysed by CDPSs. CDPSs use activated amino acids, in the form of aa-tRNAs, as substrates to catalyse the formation of cyclodipeptides, also known as DKPs.

Mentions: CDPSs use previously activated amino acids in the form of aa-tRNAs and catalyse the formation of the peptide bonds of the DKP scaffold (1) (Figure 1). Only two other enzymes families also use loaded tRNA as substrates to form peptide bonds (4–7): Fem aminoacyl transferases form cross-bridges in peptidoglycan biosynthesis (8), and aa-tRNA protein transferases modify the N-terminal extremity of proteins for subsequent degradation (9). Fem aa-transferases and aa-tRNA protein transferases thus catalyse similar chemical reactions, in which the amino acid loaded on an aa-tRNA donor is transferred to the N-terminal amino group of a peptide or a protein acceptor. They both also belong to the same structural GCN5-related N-acetyltransferase (GNAT) protein superfamily (9–11). CDPSs differ from Fem aa-transferases and aa-tRNA protein transferases in that they use two aa-tRNAs to form two peptide bonds, whereas transferases use only one aa-tRNA to form only one peptide bond. CDPSs and transferases have also different structural organizations. Indeed, the crystal structure of a CDPS, namely Rv2275 of Mycobacterium tuberculosis, was recently determined (12), revealing that Rv2275 is a homodimer, each monomer being structurally related to class-Ic aminoacyl-tRNA synthetases (aaRSs) (13–16). Rv2275 uses two tyrosyl-tRNATyr (Tyr-tRNATyr) as substrates to produce cyclo(l-Tyr–l-Tyr) (cYY) (1).Figure 1.


Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis.

Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M - Nucleic Acids Res. (2011)

The reaction catalysed by CDPSs. CDPSs use activated amino acids, in the form of aa-tRNAs, as substrates to catalyse the formation of cyclodipeptides, also known as DKPs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105412&req=5

Figure 1: The reaction catalysed by CDPSs. CDPSs use activated amino acids, in the form of aa-tRNAs, as substrates to catalyse the formation of cyclodipeptides, also known as DKPs.
Mentions: CDPSs use previously activated amino acids in the form of aa-tRNAs and catalyse the formation of the peptide bonds of the DKP scaffold (1) (Figure 1). Only two other enzymes families also use loaded tRNA as substrates to form peptide bonds (4–7): Fem aminoacyl transferases form cross-bridges in peptidoglycan biosynthesis (8), and aa-tRNA protein transferases modify the N-terminal extremity of proteins for subsequent degradation (9). Fem aa-transferases and aa-tRNA protein transferases thus catalyse similar chemical reactions, in which the amino acid loaded on an aa-tRNA donor is transferred to the N-terminal amino group of a peptide or a protein acceptor. They both also belong to the same structural GCN5-related N-acetyltransferase (GNAT) protein superfamily (9–11). CDPSs differ from Fem aa-transferases and aa-tRNA protein transferases in that they use two aa-tRNAs to form two peptide bonds, whereas transferases use only one aa-tRNA to form only one peptide bond. CDPSs and transferases have also different structural organizations. Indeed, the crystal structure of a CDPS, namely Rv2275 of Mycobacterium tuberculosis, was recently determined (12), revealing that Rv2275 is a homodimer, each monomer being structurally related to class-Ic aminoacyl-tRNA synthetases (aaRSs) (13–16). Rv2275 uses two tyrosyl-tRNATyr (Tyr-tRNATyr) as substrates to produce cyclo(l-Tyr–l-Tyr) (cYY) (1).Figure 1.

Bottom Line: These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs.AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which L-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine.These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.

View Article: PubMed Central - PubMed

Affiliation: CEA, IBITECS, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France.

ABSTRACT
Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which L-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.

Show MeSH