+Open data
-Basic information
Entry | Database: PDB / ID: 8i4z | ||||||
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Title | CalA3 with hydrolysis product | ||||||
Components | Beta-ketoacyl-acyl-carrier-protein synthase I | ||||||
Keywords | TRANSFERASE / polyketide synthase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase I / DIM/DIP cell wall layer assembly / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces chartreusis NRRL 3882 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å | ||||||
Authors | Wang, J. / Wang, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: C-N bond formation by a polyketide synthase. Authors: Jialiang Wang / Xiaojie Wang / Xixi Li / LiangLiang Kong / Zeqian Du / Dandan Li / Lixia Gou / Hao Wu / Wei Cao / Xiaozheng Wang / Shuangjun Lin / Ting Shi / Zixin Deng / Zhijun Wang / Jingdan Liang / Abstract: Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the ...Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i4z.cif.gz | 1013.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i4z.ent.gz | 827 KB | Display | PDB format |
PDBx/mmJSON format | 8i4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i4z_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8i4z_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8i4z_validation.xml.gz | 94.4 KB | Display | |
Data in CIF | 8i4z_validation.cif.gz | 146.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/8i4z ftp://data.pdbj.org/pub/pdb/validation_reports/i4/8i4z | HTTPS FTP |
-Related structure data
Related structure data | 35189MC 7wvzC 8i4yC C: citing same article (ref.) M: map data used to model this data |
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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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-Components
#1: Protein | Mass: 178383.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces chartreusis NRRL 3882 (bacteria) Gene: SCNRRL3882_6975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N9BJK0 #2: Chemical | ChemComp-ONF / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CalA3, a polyketide synthase catalyzing C-N bond formation Type: CELL / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Streptomyces chartreusis NRRL 3882 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 48.06 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141918 / Symmetry type: POINT |