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- EMDB-17119: 24-meric catalytic domain of dihydrolipoamide acetyltransferase (... -

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Basic information

Entry
Database: EMDB / ID: EMD-17119
Title24-meric catalytic domain of dihydrolipoamide acetyltransferase (E2) of the E. coli pyruvate dehydrogenase complex.
Map data
Sample
  • Complex: 24-meric catalytic domain of dihydrolipoamide acetyltransferase (E2) of the E. coli pyruvate dehydrogenase complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complexDihydrolipoyl transacetylase
Keywordspyruvate dehydrogenase complex / PDHc / E2 / cryo-EM / TRANSFERASE
Function / homology
Function and homology information


pyruvate catabolic process / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / lipoic acid binding / pyruvate dehydrogenase complex / pyruvate metabolic process / acetyltransferase activity / glycolytic process / cytoplasm
Similarity search - Function
Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme ...Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZdanowicz R / Meinhold S / Glockshuber R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Sci Adv / Year: 2024
Title: Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex.
Authors: Sarah Meinhold / Rafal Zdanowicz / Christoph Giese / Rudi Glockshuber /
Abstract: The pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). ...The pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The PDHc core is a cubic complex of eight E2 homotrimers. Homodimers of the peripheral subunits E1 and E3 associate with the core by binding to the peripheral subunit binding domain (PSBD) of E2. Previous reports indicated that 12 E1 dimers and 6 E3 dimers bind to the 24-meric E2 core. Using an assembly arrested E2 homotrimer (E2), we show that two of the three PSBDs in the E2 dimerize, that each PSBD dimer cooperatively binds two E1 dimers, and that E3 dimers only bind to the unpaired PSBD in E2. This mechanism is preserved in wild-type PDHc, with an E1 dimer:E2 monomer:E3 dimer stoichiometry of 16:24:8. The conserved PSBD dimer interface indicates that PSBD dimerization is the previously unrecognized architectural determinant of gammaproteobacterial PDHc megacomplexes.
History
DepositionApr 13, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17119.png

Downloads & links

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Map

FileDownload / File: emd_17119.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 302.387 Å		1.18 Å/pix.
x 256 pix.
= 302.387 Å		1.18 Å/pix.
x 256 pix.
= 302.387 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1812 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.2825289 - 5.1489077
Average (Standard dev.)0.017449565 (±0.1569372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 302.3872 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17119_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17119_half_map_2.map
Projections & Slices
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Sample components

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Entire : 24-meric catalytic domain of dihydrolipoamide acetyltransferase (...

EntireName: 24-meric catalytic domain of dihydrolipoamide acetyltransferase (E2) of the E. coli pyruvate dehydrogenase complex
Components
  • Complex: 24-meric catalytic domain of dihydrolipoamide acetyltransferase (E2) of the E. coli pyruvate dehydrogenase complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complexDihydrolipoyl transacetylase

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Supramolecule #1: 24-meric catalytic domain of dihydrolipoamide acetyltransferase (...

SupramoleculeName: 24-meric catalytic domain of dihydrolipoamide acetyltransferase (E2) of the E. coli pyruvate dehydrogenase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Wild-type E2 protein was truncated to contain only the catalytic domain
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 660 KDa

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Macromolecule #1: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...

MacromoleculeName: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.491049 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GIPGMLPWPK VDFSKFGEIE EVELGRIQKI SGANLSRNWV MIPHVTHFDK TDITELEAFR KQQNEEAAKR KLDVKITPVV FIMKAVAAA LEQMPRFNSS LSEDGQRLTL KKYINIGVAV DTPNGLVVPV FKDVNKKGII ELSRELMTIS KKARDGKLTA G EMQGGCFT ...String:
GIPGMLPWPK VDFSKFGEIE EVELGRIQKI SGANLSRNWV MIPHVTHFDK TDITELEAFR KQQNEEAAKR KLDVKITPVV FIMKAVAAA LEQMPRFNSS LSEDGQRLTL KKYINIGVAV DTPNGLVVPV FKDVNKKGII ELSRELMTIS KKARDGKLTA G EMQGGCFT ISSIGGLGTT HFAPIVNAPE VAILGVSKSA MEPVWNGKEF VPRLMLPISL SFDHRVIDGA DGARFITIIN NT LSDIRRL VM

UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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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: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC Ab-Initio model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 278268
FSC plot (resolution estimation)

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