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- EMDB-28890: Cryo-EM structure of alkane 1-monooxygenase AlkB-AlkG complex fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-28890
TitleCryo-EM structure of alkane 1-monooxygenase AlkB-AlkG complex from Fontimonas thermophila
Map data
Sample
  • Complex: Electron transfer complex of AlkB and AlkG
    • Protein or peptide: Alkane 1-monooxygenase
  • Ligand: FE (III) ION
  • Ligand: DODECANE
KeywordsElectron transfer complex / iron-sulfur cluster / histidine-diiron center / hydrophobic alkane binding pocket / OXIDOREDUCTASE
Function / homology
Function and homology information


monooxygenase activity / lipid metabolic process / iron ion binding / plasma membrane
Similarity search - Function
Alkane/xylene monooxygenase / Fatty acid desaturase domain / Fatty acid desaturase / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
Alkane 1-monooxygenase
Similarity search - Component
Biological speciesFontimonas thermophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsChai J / Guo G / McSweeney S / Shanklin J / Liu Q
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: 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
DepositionNov 17, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28890.png

Downloads & links

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Map

FileDownload / File: emd_28890.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 128 pix.
= 170.496 Å		1.33 Å/pix.
x 128 pix.
= 170.496 Å		1.33 Å/pix.
x 128 pix.
= 170.496 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.72
Minimum - Maximum-1.4733763 - 3.1035407
Average (Standard dev.)0.00767573 (±0.11410744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 170.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28890_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28890_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 : Electron transfer complex of AlkB and AlkG

EntireName: Electron transfer complex of AlkB and AlkG
Components
  • Complex: Electron transfer complex of AlkB and AlkG
    • Protein or peptide: Alkane 1-monooxygenase
  • Ligand: FE (III) ION
  • Ligand: DODECANE

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Supramolecule #1: Electron transfer complex of AlkB and AlkG

SupramoleculeName: Electron transfer complex of AlkB and AlkG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Fontimonas thermophila (bacteria)

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Macromolecule #1: Alkane 1-monooxygenase

MacromoleculeName: Alkane 1-monooxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: alkane 1-monooxygenase
Source (natural)Organism: Fontimonas thermophila (bacteria)
Molecular weightTheoretical: 52.942164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMSTPTLD AGTLAWNDGK RYLWLLSPFI PVLGLIGLGL FLYTDIGLFT WSGPLLIYGL IPLLDWLVGE DRNNPPEAAV AQLENDRYY RAIVYAYLPT QYAVTVLGTW VAVTADLAIW EYIGLVLSVG AVNGIGINTA HELGHKRENL DRWLAKLTLA P VAYGHFFV ...String:
SNAMSTPTLD AGTLAWNDGK RYLWLLSPFI PVLGLIGLGL FLYTDIGLFT WSGPLLIYGL IPLLDWLVGE DRNNPPEAAV AQLENDRYY RAIVYAYLPT QYAVTVLGTW VAVTADLAIW EYIGLVLSVG AVNGIGINTA HELGHKRENL DRWLAKLTLA P VAYGHFFV EHNRGHHKNV ATPEDPASSK MGESFWAFLP RTVIGSLRSA WAIEKARLQR NKQSVWSLDN ENLQAWAMTI VL FGALTAC LGWPALLFLV LQAAYGASLL EVINYIEHYG LLRQKLPDGR YERCQPRHSW NSNHIVTNLF LYQLQRHSDH HAN PTRRFQ ALRHFDDSPQ LPSGYASMLI PAYVPWLWFR LMDPLVARHY GGDLTKANLY PPKRAALLAR WHRPRPDARR ADTQ PTDAT ATPADAAASP GGRYQCTDCG YIYDEAIGCP REGFPPGTPW SQIPDDWSCP DCAVRDKVDF RKLPAA

UniProtKB: Alkane 1-monooxygenase

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 3 / Number of copies: 1 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46953
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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