3s7t

Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic

spinqualitylabelsall models 3s7t, resolution 2.81Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3s7t is a 2 chain structure with sequence from Bacld. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. NonStd Res: MSE Related: 3oqh, 3oqi, 3oqj Gene: BL00817, BLi03566, yvmC (BACLD) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [CDLS_BACLD] Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. 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-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and methionine, into cyclodipeptides. Publication Abstract from PubMed Cyclodipeptides are secondary metabolites biosynthesized by many bacteria and exhibit a wide array of biological activities. Recently, a new class of small proteins, named cyclodipeptide synthases (CDPS), which are unrelated to the typical nonribosomal peptide synthetases, was shown to generate several cyclodipeptides, using aminoacyl-tRNAs as substrates. The Mycobacterium tuberculosis CDPS, Rv2275, was found to generate cyclodityrosine through the formation of an aminoacyl-enzyme intermediate and to have a structure and oligomeric state similar to those of the class Ic aminoacyl-tRNA synthetases (aaRSs). However, the poor sequence conservation among CDPSs has raised questions about the architecture and catalytic mechanism of the identified homologs. Here we report the crystal structures of Bacillus licheniformis CDPS YvmC-Blic, in the apo form and complexed with substrate mimics, at 1.7-2.4-A resolutions. The YvmC-Blic structure also exhibits similarity to the class Ic aaRSs catalytic domain. Our mutational analysis confirmed the importance of a set of residues for cyclodileucine formation among the conserved residues localized in the catalytic pocket. Our biochemical data indicated that YvmC-Blic binds tRNA and generates cyclodileucine as a monomer. We were also able to detect the presence of an aminoacyl-enzyme reaction intermediate, but not a dipeptide tRNA intermediate, whose existence was postulated for Rv2275. Instead, our results support a sequential catalytic mechanism for YvmC-Blic, with the successive attachment of two leucine residues on the enzyme via a conserved serine residue. Altogether, our findings suggest that all CDPS enzymes share a common aaRS-like architecture and a catalytic mechanism involving the formation of an enzyme-bound intermediate. Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.,Bonnefond L, Arai T, Sakaguchi Y, Suzuki T, Ishitani R, Nureki O Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3912-7. Epub 2011 Feb 15. PMID:21325056 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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