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Structure paper

TitleProduct analog binding identifies the copper active site of particulate methane monooxygenase.
Journal, issue, pagesNat Catal, Vol. 6, Issue 12, Page 1194-1204, Year 2023
Publish dateNov 6, 2023
AuthorsFrank J Tucci / Richard J Jodts / Brian M Hoffman / Amy C Rosenzweig /
PubMed AbstractNature'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.
External linksNat Catal / PubMed:38187819 / PubMed Central
MethodsEM (single particle)
Resolution2.16 - 3.22 Å
Structure data

17287

8oyi

EMDB-17287, PDB-8oyi:
particulate methane monooxygenase with 2,2,2-trifluoroethanol bound
Method: EM (single particle) / Resolution: 2.19 Å

40714

8sqw

EMDB-40714, PDB-8sqw:
particulate methane monooxygenase crosslinked with 2,2,2-trifluoroethanol bound
Method: EM (single particle) / Resolution: 2.16 Å

40717

8sr1

EMDB-40717, PDB-8sr1:
particulate methane monooxygenase crosslinked with 4,4,4-trifluorobutanol bound
Method: EM (single particle) / Resolution: 2.18 Å

40719

8sr4

EMDB-40719, PDB-8sr4:
particulate methane monooxygeanse treated with potassium cyanide and copper reloaded
Method: EM (single particle) / Resolution: 3.12 Å

40720

8sr5

EMDB-40720, PDB-8sr5:
particulate methane monooxygenase potassium cyanide treated
Method: EM (single particle) / Resolution: 3.22 Å

Chemicals

ChemComp-CU:
COPPER (II) ION / Copper

ChemComp-D10:
DECANE / Decane

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

ChemComp-P1O:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DDPC, phospholipid*YM

ChemComp-HXG:
1,2-dihexanoyl-sn-glycero-3-phosphocholine

ChemComp-ETF:
TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol

ChemComp-HOH:
WATER / Water

ChemComp-WIY:
4,4,4-trifluorobutan-1-ol

Source
  • methylococcus capsulatus str. bath (bacteria)
  • methylococcus capsulatus (bacteria)
KeywordsOXIDOREDUCTASE / Metalloenzyme / Membrane Protein / Inhibitor / Nanodisc / Nanodiscs / Active Site

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