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Yorodumi- PDB-6ltb: Crystal Structure of Nonribosomal peptide synthetases (NRPS), Fmo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ltb | ||||||||||||
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Title | Crystal Structure of Nonribosomal peptide synthetases (NRPS), FmoA3 (S1046A)-AMPPNP bound form | ||||||||||||
Components | Nonribosomal peptide synthetaseNonribosomal peptide | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetases (NRPS) / JBIR-34 and -35 | ||||||||||||
Function / homology | Function and homology information organic cyclic compound biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity Similarity search - Function | ||||||||||||
Biological species | Streptomyces sp. Sp080513GE-23 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||
Authors | Senda, T. / Harada, A. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Angew Chem Int Ed Engl / Year: 2021 Title: Structural and Functional Analyses of the Tridomain-Nonribosomal Peptide Synthetase FmoA3 for 4-Methyloxazoline Ring Formation. Authors: Yohei Katsuyama / Kaoru Sone / Ayaka Harada / Seiji Kawai / Naoki Urano / Naruhiko Adachi / Toshio Moriya / Masato Kawasaki / Kazuo Shin-Ya / Toshiya Senda / Yasuo Ohnishi / Abstract: Nonribosomal peptide synthetases (NRPSs) are attractive targets for bioengineering to generate useful peptides. FmoA3 is a single modular NRPS composed of heterocyclization (Cy), adenylation (A), and ...Nonribosomal peptide synthetases (NRPSs) are attractive targets for bioengineering to generate useful peptides. FmoA3 is a single modular NRPS composed of heterocyclization (Cy), adenylation (A), and peptidyl carrier protein (PCP) domains. It uses α-methyl-l-serine to synthesize a 4-methyloxazoline ring, probably with another Cy domain in the preceding module FmoA2. Here, we determined the head-to-tail homodimeric structures of FmoA3 by X-ray crystallography (apo-form, with adenylyl-imidodiphosphate and α-methyl-l-seryl-AMP) and cryogenic electron microscopy single particle analysis, and performed site-directed mutagenesis experiments. The data revealed that α-methyl-l-serine can be accommodated in the active site because of the extra space around Ala688. The Cy domains of FmoA2 and FmoA3 catalyze peptide bond formation and heterocyclization, respectively. FmoA3's Cy domain seems to lose its donor PCP binding activity. The collective data support a proposed catalytic cycle of FmoA3. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ltb.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ltb.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ltb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6ltb ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6ltb | HTTPS FTP |
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-Related structure data
Related structure data | 6ltaSC 6ltcC 6ltdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 125243.695 Da / Num. of mol.: 1 / Mutation: S1046A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. Sp080513GE-23 (bacteria) Gene: fmoA3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A077JG85 |
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#2: Chemical | ChemComp-ANP / |
#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: 3.44 Å3/Da / Density % sol: 64.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M HEPES pH 8.0, 0.2M MgCl2, 15% Poly(acrylic acid sodium salt) 5100 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 9, 2017 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.69 Å / Num. obs: 30934 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 48.57 Å2 / CC1/2: 0.982 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.1→3.27 Å / Num. unique obs: 4446 / CC1/2: 0.75 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LTA Resolution: 3.1→49.69 Å / SU ML: 0.4185 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.155
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→49.69 Å
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Refine LS restraints |
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LS refinement shell |
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