3oqv | pdb_00003oqv
AlbC, a cyclodipeptide synthase from Streptomyces noursei
Structural highlights
Function[CLPS_STRNR] Involved in the biosynthesis of albonoursin (cyclo[(alpha,beta-dehydro-Phe)-(alpha,beta-dehydro-Leu)]), an antibacterial peptide. It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Phe-L-Leu) (cFL) as major products from L-L-phenylalanyl-tRNA(Phe) and L-leucyl-tRNA(Leu). AlbC can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine, L-tyrosine and L-methionine, and to a much lesser extent L-alanine and L-valine, into cyclodipeptides. Indeed, ten possible cyclodipeptides composed of L-phenylalanine, L-leucine, L-tyrosine and L-methionine are all synthesized to detectable amounts by AlbC.[1] [2] Publication Abstract from PubMedCyclodipeptide 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. 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 May 1;39(10):4475-89. Epub 2011 Feb 3. PMID:21296757[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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