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- PDB-7ly6: Structure of a trans-acting NRPS oxidase, BmdC, involved in bacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ly6 | ||||||
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Title | Structure of a trans-acting NRPS oxidase, BmdC, involved in bacillamide biosynthesis | ||||||
![]() | BmdC, NRPS oxidase | ||||||
![]() | FLAVOPROTEIN / Nonribosomal peptide synthetases Bacillamide | ||||||
Function / homology | FLAVIN MONONUCLEOTIDE / GLYCINE / PHOSPHATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fortinez, C.M. / Bloudoff, K. / Schmeing, T.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Authors: Camille Marie Fortinez / Kristjan Bloudoff / Connor Harrigan / Itai Sharon / Mike Strauss / T Martin Schmeing / ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 227.1 KB | Display | ![]() |
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PDB format | ![]() | 165.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 795.6 KB | Display | ![]() |
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Full document | ![]() | 797.7 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ly4C ![]() 7ly5C ![]() 7ly7C ![]() 3eo7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38177.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 35% PEG1500 (wt/vol), 0.1M SPG buffer pH9.0. [1M SPG buffer: (1.48g of succinic acid, 6.04g sodium dihydrogen phosphate monohydrate and 3.28g of glycine in 100ml of water)] |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→94.08 Å / Num. obs: 29493 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 55.83 Å2 / Rmerge(I) obs: 0.249 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 2.73→2.86 Å / Num. unique obs: 29506 / CC1/2: 0.354 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EO7 Resolution: 2.73→94.07 Å / SU ML: 0.3065 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.928 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→94.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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