5TXE
AtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound
Summary for 5TXE
| Entry DOI | 10.2210/pdb5txe/pdb |
| Related | 5TXC |
| Descriptor | AtxE2, Astexin3-dC4 (3 entities in total) |
| Functional Keywords | isopeptidase, lasso peptide, natural product, hydrolase |
| Biological source | Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48) More |
| Total number of polymer chains | 4 |
| Total formula weight | 162453.18 |
| Authors | Chekan, J.R.,Nair, S.K. (deposition date: 2016-11-16, release date: 2016-12-21, Last modification date: 2024-10-23) |
| Primary citation | Chekan, J.R.,Koos, J.D.,Zong, C.,Maksimov, M.O.,Link, A.J.,Nair, S.K. Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. J. Am. Chem. Soc., 138:16452-16458, 2016 Cited by PubMed Abstract: Lasso peptides are a class of bioactive ribosomally synthesized and post-translationally modified peptides (RiPPs), with a threaded knot structure that is formed by an isopeptide bond attaching the N-terminus of the peptide to a side chain carboxylate. Some lasso peptide biosynthetic clusters harbor an enzyme that specifically hydrolyzes the isopeptide bond to yield the linear peptide. We describe here the 2.4 Å resolution structure of a lasso peptide isopeptidase revealing a topologically novel didomain architecture consisting of an open β-propeller appended to an α/β hydrolase domain. The 2.2 Å resolution cocrystal structure of an inactive variant in complex with a lasso peptide reveals deformation of the substrate, and reorganization of the enzyme active site, which exposes and orients the isopeptide bond for hydrolysis. Structure-based mutational analysis reveals how this enzyme recognizes the lasso peptide substrate by shape complementarity rather than through sequence specificity. The isopeptidase gene can be used to facilitate genome mining, as a network-based mining strategy queried with this sequence identified 87 putative lasso peptide biosynthetic clusters, 65 of which have not been previously described. Lastly, we validate this mining approach by heterologous expression of two clusters encoded within the genome of Asticcaucalis benevestitus, and demonstrate that both clusters produce lasso peptides. PubMed: 27998080DOI: 10.1021/jacs.6b10389 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.2 Å) |
Structure validation
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