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Yorodumi- PDB-8f6t: Cryo-EM structure of alkane 1-monooxygenase AlkB-AlkG complex fro... -
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-Basic information
Entry | Database: PDB / ID: 8f6t | ||||||
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Title | Cryo-EM structure of alkane 1-monooxygenase AlkB-AlkG complex from Fontimonas thermophila | ||||||
Components | Alkane 1-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Electron transfer complex / iron-sulfur cluster / histidine-diiron center / hydrophobic alkane binding pocket | ||||||
Function / homology | Function and homology information monooxygenase activity / lipid metabolic process / iron ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Fontimonas thermophila (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Chai, J. / Guo, G. / McSweeney, S. / Shanklin, J. / Liu, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structural basis for enzymatic terminal C-H bond functionalization of alkanes. Authors: Jin Chai / Gongrui Guo / Sean M McSweeney / John Shanklin / Qun Liu / Abstract: Alkane monooxygenase (AlkB) is a widely occurring integral membrane metalloenzyme that catalyzes the initial step in the functionalization of recalcitrant alkanes with high terminal selectivity. AlkB ...Alkane monooxygenase (AlkB) is a widely occurring integral membrane metalloenzyme that catalyzes the initial step in the functionalization of recalcitrant alkanes with high terminal selectivity. AlkB enables diverse microorganisms to use alkanes as their sole carbon and energy source. Here we present the 48.6-kDa cryo-electron microscopy structure of a natural fusion from Fontimonas thermophila between AlkB and its electron donor AlkG at 2.76 Å resolution. The AlkB portion contains six transmembrane helices with an alkane entry tunnel within its transmembrane domain. A dodecane substrate is oriented by hydrophobic tunnel-lining residues to present a terminal C-H bond toward a diiron active site. AlkG, an [Fe-4S] rubredoxin, docks via electrostatic interactions and sequentially transfers electrons to the diiron center. The archetypal structural complex presented reveals the basis for terminal C-H selectivity and functionalization within this broadly distributed evolutionary class of enzymes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8f6t.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f6t.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/8f6t ftp://data.pdbj.org/pub/pdb/validation_reports/f6/8f6t | HTTPS FTP |
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-Related structure data
Related structure data | 28890MC 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: 52942.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fontimonas thermophila (bacteria) / Gene: SAMN04488120_10311 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I2I8Z9, alkane 1-monooxygenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-D12 / | Has ligand of interest | Y | |
-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: Electron transfer complex of AlkB and AlkG / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Fontimonas thermophila (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
Specimen | 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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46953 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.93 Å2 | ||||||||||||||||||||||||
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