title: Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis.
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.
authors.affiliation: CEA, IBITECS, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Sauguet
authors.forename: Mireille
authors.initials: M
authors.lastname: Moutiez
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Pascal
authors.initials: P
authors.lastname: Belin
authors.forename: Jérôme
authors.initials: J
authors.lastname: Seguin
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Le Du
authors.forename: Robert
authors.initials: R
authors.lastname: Thai
authors.forename: Cédric
authors.initials: C
authors.lastname: Masson
authors.forename: Matthieu
authors.initials: M
authors.lastname: Fonvielle
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Pernodet
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Charbonnier
authors.forename: Muriel
authors.initials: M
authors.lastname: Gondry
mesh_terms: D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D055162:Biocatalysis; D020134:Catalytic Domain; D003461:Crystallography; D004151:Dipeptides / Q000096:biosynthesis*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D046908:Peptide Biosynthesis, Nucleic Acid-Independent; D010453:Peptide Synthases / Q000737:chemistry* / Q000378:metabolism; D010456:Peptides, Cyclic / Q000096:biosynthesis*; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013302:Streptomyces / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D004151:Dipeptides; D010456:Peptides, Cyclic; D012346:RNA, Transfer, Amino Acyl; D000604:Amino Acyl-tRNA Synthetases; D010453:Peptide Synthases