Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 548, Year 2022
Publish date	Jan 27, 2022
Authors	Camille Marie Fortinez / Kristjan Bloudoff / Connor Harrigan / Itai Sharon / Mike Strauss / T Martin Schmeing /
PubMed Abstract	Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and ...Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
External links	Nat Commun / PubMed:35087027 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.5 - 4.2 Å
Structure data	23587 7ly4 EMDB-23587, PDB-7ly4: Cryo-EM structure of the elongation module of the bacillamide NRPS, BmdB, in complex with the oxidase, BmdC Method: EM (single particle) / Resolution: 3.8 Å EMDB-23588: Cryo-EM map of the elongation module of the bacillamide NRPS, BmdB, complexed with the oxidase BmdC Method: EM (single particle) / Resolution: 4.2 Å PDB-7ly5: Proteolyzed crystal structure of the bacillamide NRPS, BmdB, in complex with the oxidase BmdC Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-7ly6: Structure of a trans-acting NRPS oxidase, BmdC, involved in bacillamide biosynthesis Method: X-RAY DIFFRACTION / Resolution: 2.73 Å PDB-7ly7: Crystal structure of the elongation module of the bacillamide NRPS, BmdB, in complex with the oxidase BmdC Method: X-RAY DIFFRACTION / Resolution: 3.8 Å
Chemicals	ChemComp-FMN: FLAVIN MONONUCLEOTIDE / Flavin mononucleotide ChemComp-HOH: WATER / Water ChemComp-GLY: GLYCINE / Glycine ChemComp-PO4: PHOSPHATE ION / Phosphate ChemComp-YOA: 5'-{[(2R,3S)-3-amino-2-({2-[(N-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-4-sulfanylbutane-1-sulfonyl]amino}-5'-deoxyadenosine
Source	thermoactinomyces vulgaris (bacteria)
Keywords	BIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetases Oxidase Bacillamide synthetases / BIOSYNTHETIC PROTEIN/OXIDOREDUCTASE / Nonribosomal peptide synthetases / Bacillamide / FLAVOPROTEIN / BIOSYNTHETIC PROTEIN-OXIDOREDUCTASE complex / Nonribosomal peptide synthetases Bacillamide