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- EMDB-16217: Escherichia coli anaerobic fatty acid beta oxidation trifunctiona... -

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Basic information

Entry
Database: EMDB / ID: EMD-16217
TitleEscherichia coli anaerobic fatty acid beta oxidation trifunctional enzyme (anEcTFE) trimeric complex
Map dataAnEcTFE A2B
Sample
  • Complex: anEcTFE trimer
    • Protein or peptide: 3-ketoacyl-CoA thiolase FadI
    • Protein or peptide: Fatty acid oxidation complex subunit alphaBeta oxidation
Keywordscomplex / heterotrimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


fatty acid beta-oxidation, unsaturated, even number / fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity ...fatty acid beta-oxidation, unsaturated, even number / fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytosol / cytoplasm
Similarity search - Function
Acetyl-CoA C-acyltransferase FadI / Fatty oxidation complex, alpha subunit FadJ / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. ...Acetyl-CoA C-acyltransferase FadI / Fatty oxidation complex, alpha subunit FadJ / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-ketoacyl-CoA thiolase FadI / Fatty acid oxidation complex subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsSah-Teli SK / Pinkas M / Novacek J / Venkatesan R
Funding support Czech Republic, Finland, European Union, 3 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
Academy of Finland293369, 289024 and 319194 Finland
H2020 Marie Curie Actions of the European Commission871037, 871037European Union
CitationJournal: Structure / Year: 2023
Title: Structural basis for different membrane-binding properties of E. coli anaerobic and human mitochondrial β-oxidation trifunctional enzymes.
Authors: Shiv K Sah-Teli / Matyas Pinkas / Mikko J Hynönen / Sarah J Butcher / Rik K Wierenga / Jiri Novacek / Rajaram Venkatesan /
Abstract: Facultative anaerobic bacteria such as Escherichia coli have two αβ heterotetrameric trifunctional enzymes (TFE), catalyzing the last three steps of the β-oxidation cycle: soluble aerobic TFE ...Facultative anaerobic bacteria such as Escherichia coli have two αβ heterotetrameric trifunctional enzymes (TFE), catalyzing the last three steps of the β-oxidation cycle: soluble aerobic TFE (EcTFE) and membrane-associated anaerobic TFE (anEcTFE), closely related to the human mitochondrial TFE (HsTFE). The cryo-EM structure of anEcTFE and crystal structures of anEcTFE-α show that the overall assembly of anEcTFE and HsTFE is similar. However, their membrane-binding properties differ considerably. The shorter A5-H7 and H8 regions of anEcTFE-α result in weaker α-β as well as α-membrane interactions, respectively. The protruding H-H region of anEcTFE-β is therefore more critical for membrane-association. Mutational studies also show that this region is important for the stability of the anEcTFE-β dimer and anEcTFE heterotetramer. The fatty acyl tail binding tunnel of the anEcTFE-α hydratase domain, as in HsTFE-α, is wider than in EcTFE-α, accommodating longer fatty acyl tails, in good agreement with their respective substrate specificities.
History
DepositionNov 23, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16217.png

Downloads & links

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Map

FileDownload / File: emd_16217.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnEcTFE A2B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.21385792 - 0.54201907
Average (Standard dev.)0.0010665527 (±0.013765607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: AnEcTFE A2B hal f2

Fileemd_16217_half_map_1.map
AnnotationAnEcTFE A2B hal f2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AnEcTFE A2B half 1

Fileemd_16217_half_map_2.map
AnnotationAnEcTFE A2B half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : anEcTFE trimer

EntireName: anEcTFE trimer
Components
  • Complex: anEcTFE trimer
    • Protein or peptide: 3-ketoacyl-CoA thiolase FadI
    • Protein or peptide: Fatty acid oxidation complex subunit alphaBeta oxidation

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Supramolecule #1: anEcTFE trimer

SupramoleculeName: anEcTFE trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: heterotrimeric complex
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: 3-ketoacyl-CoA thiolase FadI

MacromoleculeName: 3-ketoacyl-CoA thiolase FadI / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetyl-CoA C-acyltransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.20207 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SQDPMGQVLP LVTRQGDRIA IVSGLRTPFA RQATAFHGIP AVDLGKMVVG ELLARSEIPA EVIEQLVFGQ VVQMPEAPN IAREIVLGTG MNVHTDAYSV SRACATSFQA VANVAESLMA GTIRAGIAGG ADSSSVLPIG VSKKLARVLV D VNKARTMS ...String:
MGSSHHHHHH SQDPMGQVLP LVTRQGDRIA IVSGLRTPFA RQATAFHGIP AVDLGKMVVG ELLARSEIPA EVIEQLVFGQ VVQMPEAPN IAREIVLGTG MNVHTDAYSV SRACATSFQA VANVAESLMA GTIRAGIAGG ADSSSVLPIG VSKKLARVLV D VNKARTMS QRLKLFSRLR LRDLMPVPPA VAEYSTGLRM GDTAEQMAKT YGITREQQDA LAHRSHQRAA QAWSDGKLKE EV MTAFIPP YKQPLVEDNN IRGNSSLADY AKLRPAFDRK HGTVTAANST PLTDGAAAVI LMTESRAKEL GLVPLGYLRS YAF TAIDVW QDMLLGPAWS TPLALERAGL TMSDLTLIDM HEAFAAQTLA NIQLLGSERF AREALGRAHA TGEVDDSKFN VLGG SIAYG HPFAATGARM ITQTLHELRR RGGGFGLVTA CAAGGLGAAM VLEAE

UniProtKB: 3-ketoacyl-CoA thiolase FadI

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Macromolecule #2: Fatty acid oxidation complex subunit alpha

MacromoleculeName: Fatty acid oxidation complex subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: enoyl-CoA hydratase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 77.169125 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQ GQQLMAEIHA LPIQVIAAIH GACLGGGLEL ALACHGRVCT DDPKTVLGLP EVQLGLLPGS GGTQRLPRLI G VSTALEMI ...String:
MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQ GQQLMAEIHA LPIQVIAAIH GACLGGGLEL ALACHGRVCT DDPKTVLGLP EVQLGLLPGS GGTQRLPRLI G VSTALEMI LTGKQLRAKQ ALKLGLVDDV VPHSILLEAA VELAKKERPS SRPLPVRERI LAGPLGRALL FKMVGKKTEH KT QGNYPAT ERILEVVETG LAQGTSSGYD AEARAFGELA MTPQSQALRS IFFASTDVKK DPGSDAPPAP LNSVGILGGG LMG GGIAYV TACKAGIPVR IKDINPQGIN HALKYSWDQL EGKVRRRHLK ASERDKQLAL ISGTTDYRGF AHRDLIIEAV FENL ELKQQ MVAEVEQNCA AHTIFASNTS SLPIGDIAAH ATRPEQVIGL HFFSPVEKMP LVEIIPHAGT SAQTIATTVK LAKKQ GKTP IVVRDKAGFY VNRILAPYIN EAIRMLTQGE RVEHIDAALV KFGFPVGPIQ LLDEVGIDTG TKIIPVLEAA YGERFS APA NVVSSILNDD RKGRKNGRGF YLYGQKGRKS KKQVDPAIYP LIGTQGQGRI SAPQVAERCV MLMLNEAVRC VDEQVIR SV RDGDIGAVFG IGFPPFLGGP FRYIDSLGAG EVVAIMQRLA TQYGSRFTPC ERLVEMGARG ESFWKTTATD LQ

UniProtKB: Fatty acid oxidation complex subunit alpha

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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

Concentration0.1 mg/mL
BufferpH: 8
Details: 50 mM Tris, 500 mM NaCl, 5% glycerol, 2.5 mM DTT, 0.0033% amphipol A8-35, pH 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GRAPHENE / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 3 / Number real images: 18669 / Average exposure time: 5.0 sec. / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final 3D classificationSoftware: (Name: RELION, cryoSPARC)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 37357
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Target criteria: cross-correlation coefficient
Output model

PDB-8brj:
Escherichia coli anaerobic fatty acid beta oxidation trifunctional enzyme (anEcTFE) trimeric complex

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