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Yorodumi- PDB-8f7h: The condensation domain of surfactin A synthetase C variant 18b i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f7h | ||||||
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Title | The condensation domain of surfactin A synthetase C variant 18b in space group P212121 | ||||||
Components | Surfactin synthetase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / NRPS / C domain / SrfA-C | ||||||
Function / homology | Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / catalytic activity / Surfactin synthetase Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Frota, N.F. / Pistofidis, A. / Folger, I.B. / Hilvert, D. / Schmeing, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: High-throughput reprogramming of an NRPS condensation domain. Authors: Ines B Folger / Natália F Frota / Angelos Pistofidis / David L Niquille / Douglas A Hansen / T Martin Schmeing / Donald Hilvert / Abstract: Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the ...Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C-domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Because C domains can function as selectivity filters in NRPSs, this methodology should facilitate the precision engineering of these molecular assembly lines. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f7h.cif.gz | 327.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f7h.ent.gz | 223.3 KB | Display | PDB format |
PDBx/mmJSON format | 8f7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f7h_validation.pdf.gz | 688.6 KB | Display | wwPDB validaton report |
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Full document | 8f7h_full_validation.pdf.gz | 694.3 KB | Display | |
Data in XML | 8f7h_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8f7h_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/8f7h ftp://data.pdbj.org/pub/pdb/validation_reports/f7/8f7h | HTTPS FTP |
-Related structure data
Related structure data | 8f7fC 8f7gC 8f7iC 2vsqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53579.785 Da / Num. of mol.: 1 / Fragment: Condensation domain, residues 7-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45676 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.04 M KH2PO4, 16 %w/v PEG 8K and 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 43869 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.46 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 13.5 % / Num. unique obs: 2156 / CC1/2: 0.39 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VSQ Resolution: 1.93→47.09 Å / SU ML: 0.2303 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.217 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→47.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.44722901559 Å / Origin y: -4.99347587703 Å / Origin z: -5.01156963979 Å
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Refinement TLS group | Selection details: all |