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- EMDB-17287: particulate methane monooxygenase with 2,2,2-trifluoroethanol bound -

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Basic information

Entry
Database: EMDB / ID: EMD-17287
Titleparticulate methane monooxygenase with 2,2,2-trifluoroethanol bound
Map data
Sample
  • Complex: particulate methane monooxygenase
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
  • Ligand: COPPER (II) ION
  • Ligand: DECANE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: TRIFLUOROETHANOL
  • Ligand: water
KeywordsMetalloenzyme / Membrane Protein / Inhibitor / Nanodisc / Oxidoreductase
Function / homology
Function and homology information


methane monooxygenase (particulate) / methane monooxygenase (soluble) / : / : / monooxygenase activity / membrane / metal ion binding
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein
Similarity search - Domain/homology
Particulate methane monooxygenase alpha subunit / Ammonia monooxygenase/methane monooxygenase, subunit C family protein / Particulate methane monooxygenase beta subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsTucci FJ / Rosenzweig AC
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118035 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111097 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM105538 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F31ES034283 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008382 United States
National Science Foundation (NSF, United States)MCB-190858 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Simons FoundationSF349247 United States
CitationJournal: 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
DepositionMay 4, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17287.png

Downloads & links

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Map

FileDownload / File: emd_17287.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 512 pix.
= 270.899 Å		0.53 Å/pix.
x 512 pix.
= 270.899 Å		0.53 Å/pix.
x 512 pix.
= 270.899 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5291 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.197
Minimum - Maximum-0.6866095 - 1.3186831
Average (Standard dev.)0.0029067907 (±0.03277145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 270.8992 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17287_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17287_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : particulate methane monooxygenase

EntireName: particulate methane monooxygenase
Components
  • Complex: particulate methane monooxygenase
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
  • Ligand: COPPER (II) ION
  • Ligand: DECANE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: TRIFLUOROETHANOL
  • Ligand: water

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Supramolecule #1: particulate methane monooxygenase

SupramoleculeName: particulate methane monooxygenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 337.11 kDa/nm

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Macromolecule #1: Particulate methane monooxygenase alpha subunit

MacromoleculeName: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 46.129746 KDa
SequenceString: MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN ...String:
MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN PVTTLTGQTV DLENYNEGNT YFWHAFWFAI GVAWIGYWSR RPIFIPRLLM VDAGRADELV SATDRKVAMG FL AATILIV VMAMSSANSK YPITIPLQAG TMRGMKPLEL PAPTVSVKVE DATYRVPGRA MRMKLTITNH GNSPIRLGEF YTA SVRFLD SDVYKDTTGY PEDLLAEDGL SVSDNSPLAP GETRTVDVTA SDAAWEVYRL SDIIYDPDSR FAGLLFFFDA TGNR QVVQI DAPLIPSFM

UniProtKB: Particulate methane monooxygenase alpha subunit

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Macromolecule #2: Particulate methane monooxygenase beta subunit

MacromoleculeName: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 28.445098 KDa
SequenceString: MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH ...String:
MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH VPVEYNGMLM SIADIQGYNY VRTGTPEYIR MVEKGTLRTF GKDVAPVSAF FSAFMSILIY FMWHFIGRWF SN ERFLQST

UniProtKB: Particulate methane monooxygenase beta subunit

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Macromolecule #3: Ammonia monooxygenase/methane monooxygenase, subunit C family protein

MacromoleculeName: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 29.839309 KDa
SequenceString: MAATTIGGAA AAEAPLLDKK WLTFALAIYT VFYLWVRWYE GVYGWSAGLD SFAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRN LAALTPREEL RRNFTHLVWL VAYAWAIYWG ASYFTEQDGT WHQTIVRDTD FTPSHIIEFY LSYPIYIITG F AAFIYAKT ...String:
MAATTIGGAA AAEAPLLDKK WLTFALAIYT VFYLWVRWYE GVYGWSAGLD SFAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRN LAALTPREEL RRNFTHLVWL VAYAWAIYWG ASYFTEQDGT WHQTIVRDTD FTPSHIIEFY LSYPIYIITG F AAFIYAKT RLPFFAKGIS LPYLVLVVGP FMILPNVGLN EWGHTFWFME ELFVAPLHYG FVIFGWLALA VMGTLTQTFY SF AQGGLGQ SLCEAVDEGL IAK

UniProtKB: Ammonia monooxygenase/methane monooxygenase, subunit C family protein

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Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 9 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #5: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 5 / Number of copies: 18 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 6 / Number of copies: 18 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #7: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 7 / Number of copies: 12 / Formula: P1O
Molecular weightTheoretical: 566.728 Da
Chemical component information

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

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Macromolecule #8: 1,2-dihexanoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1,2-dihexanoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 8 / Number of copies: 6 / Formula: HXG
Molecular weightTheoretical: 454.515 Da
Chemical component information

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

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Macromolecule #9: TRIFLUOROETHANOL

MacromoleculeName: TRIFLUOROETHANOL / type: ligand / ID: 9 / Number of copies: 3 / Formula: ETF
Molecular weightTheoretical: 100.04 Da
Chemical component information

ChemComp-ETF:
TRIFLUOROETHANOL

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 352 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7s4h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 500000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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