6ecf | pdb_00006ecf

Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group P1

spinqualitylabelsall models 6ecf, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ecf is a 12 chain structure with sequence from Streptomyces tsusimaensis and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.5Å Ligands: 2OP, DPP, DVA, VAD Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q1PSF3_9ACTN Publication Abstract from PubMed Many enzymes catalyse reactions that proceed through covalent acyl-enzyme (ester or thioester) intermediates(1). These enzymes include serine hydrolases(2,3) (encoded by one per cent of human genes, and including serine proteases and thioesterases), cysteine proteases (including caspases), and many components of the ubiquitination machinery(4,5). Their important acyl-enzyme intermediates are unstable, commonly having half-lives of minutes to hours(6). In some cases, acyl-enzyme complexes can be stabilized using substrate analogues or active-site mutations but, although these approaches can provide valuable insight(7-10), they often result in complexes that are substantially non-native. Here we develop a strategy for incorporating 2,3-diaminopropionic acid (DAP) into recombinant proteins, via expansion of the genetic code(11). We show that replacing catalytic cysteine or serine residues of enzymes with DAP permits their first-step reaction with native substrates, allowing the efficient capture of acyl-enzyme complexes that are linked through a stable amide bond. For one of these enzymes, the thioesterase domain of valinomycin synthetase(12), we elucidate the biosynthetic pathway by which it progressively oligomerizes tetradepsipeptidyl substrates to a dodecadepsipeptidyl intermediate, which it then cyclizes to produce valinomycin. By trapping the first and last acyl-thioesterase intermediates in the catalytic cycle as DAP conjugates, we provide structural insight into how conformational changes in thioesterase domains of such nonribosomal peptide synthetases control the oligomerization and cyclization of linear substrates. The encoding of DAP will facilitate the characterization of diverse acyl-enzyme complexes, and may be extended to capturing the native substrates of transiently acylated proteins of unknown function. Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.,Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW Nature. 2018 Dec 12. pii: 10.1038/s41586-018-0781-z. doi:, 10.1038/s41586-018-0781-z. PMID:30542153 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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