Journal: J Am Chem Soc / Year: 2021 Title: Copper Centers in the Cryo-EM Structure of Particulate Methane Monooxygenase Reveal the Catalytic Machinery of Methane Oxidation. Authors: W-H Chang / H-H Lin / I-K Tsai / S-H Huang / S-C Chung / I-P Tu / S S-F Yu / S I Chan / Abstract: The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room ...The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry. pMMO is a membrane-bound protein with three subunits (PmoB, PmoA, and PmoC) and 12-14 coppers distributed among different sites. X-ray crystal structures that have revealed only three mononuclear coppers at three sites have neither disclosed the location of the active site nor the catalytic mechanism of the enzyme. Here we report a cyro-EM structure of -pMMO from (Bath) at 2.5 Å, and develop quantitative electrostatic-potential profiling to scrutinize the nonprotein densities for signatures of the copper cofactors. Our results confirm a mononuclear Cu at the site, resolve two Cus at the site, and uncover additional Cu clusters at the PmoA/PmoC interface within the membrane ( site) and in the water-exposed -terminal subdomain of the PmoB ( clusters). These findings complete the minimal set of copper factors required for catalytic turnover of pMMO, offering a glimpse of the catalytic machinery for methane oxidation according to the chemical principles underlying the mechanism proposed earlier.
History
Deposition
May 20, 2021
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Header (metadata) release
Aug 4, 2021
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Map release
Aug 4, 2021
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Update
Aug 4, 2021
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Current status
Aug 4, 2021
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-60 / Number real images: 23484 / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
CTF correction
Software - Name: Gctf (ver. 1.18)
Startup model
Type of model: OTHER / Details: cryoSPARC ab-initio Reconstruction
Initial angle assignment
Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.15)
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