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Yorodumi- PDB-7u58: YcaO-mediated ATP-dependent peptidase activity in ribosomal pepti... -
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-Basic information
Entry | Database: PDB / ID: 7u58 | ||||||
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Title | YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis | ||||||
Components | MusD | ||||||
Keywords | HYDROLASE / Ripps / Ycao domain / musD / Cyanobactin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desmonostoc sp. PCC 7906 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Zheng, Y. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Chem Biol / Year: 2023 Title: YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Authors: Yiwu Zheng / Satish K Nair / Abstract: YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the ...YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u58.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u58.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 7u58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u58_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7u58_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7u58_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 7u58_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/7u58 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/7u58 | HTTPS FTP |
-Related structure data
Related structure data | 26344MC M: map data used to model this data 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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-Components
#1: Protein | Mass: 88844.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desmonostoc sp. PCC 7906 (bacteria) / Strain: PCC 7906 / Gene: musD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5Q0TWV7 #2: Chemical | #3: Chemical | ChemComp-MG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MusD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 88.76 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Desmonostoc sp. PCC 7906 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: HEPES pH 7.5. 25 mM KCl. |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 1.33 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123786 / Symmetry type: POINT |