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Yorodumi- PDB-8sr4: particulate methane monooxygeanse treated with potassium cyanide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sr4 | |||||||||||||||||||||
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Title | particulate methane monooxygeanse treated with potassium cyanide and copper reloaded | |||||||||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Metalloenzyme / Membrane Protein / Nanodiscs | |||||||||||||||||||||
Function / homology | Function and homology information methane monooxygenase (particulate) / methane monooxygenase complex / methane monooxygenase activity / methane monooxygenase (soluble) / methane monooxygenase NADH activity / methane monooxygenase NADPH activity / methane metabolic process / monooxygenase activity / membrane / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Methylococcus capsulatus (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||||||||||||||
Authors | Tucci, F.J. / Jodts, R.J. / Rosenzweig, A.C. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Nat Catal / Year: 2023 Title: Product analog binding identifies the copper active site of particulate methane monooxygenase. Authors: Frank J Tucci / Richard J Jodts / Brian M Hoffman / Amy C Rosenzweig / Abstract: Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of ...Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the Cu, Cu, and Cu sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the Cu site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating Cu and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sr4.cif.gz | 625.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sr4.ent.gz | 480.2 KB | Display | PDB format |
PDBx/mmJSON format | 8sr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/8sr4 ftp://data.pdbj.org/pub/pdb/validation_reports/sr/8sr4 | HTTPS FTP |
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-Related structure data
Related structure data | 40719MC 8oyiC 8sqwC 8sr1C 8sr5C 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: 42832.887 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath / References: UniProt: G1UBD1 #2: Protein | Mass: 28445.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: Q607G3, methane monooxygenase (particulate) #3: Protein | Mass: 27656.840 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath / References: UniProt: Q603F1 #4: Chemical | ChemComp-CU / 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: particulate methane monooxygenaseMethane monooxygenase (particulate) Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Molecular weight | Value: 337.11 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Methylococcus capsulatus (bacteria) / Strain: Bath |
Buffer solution | pH: 7.3 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 53.56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 864874 / Symmetry type: POINT | ||||||||||||||||||||||||
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