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- PDB-7uom: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruva... -

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Basic information

Entry
Database: PDB / ID: 7uom
TitleEndogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
ComponentsAcetyltransferase component of pyruvate dehydrogenase complex
KeywordsTRANSFERASE / e2 / pyruvate / dehydrogenase / complex
Function / homology
Function and homology information


Signaling by Retinoic Acid / Pyruvate metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Glyoxylate metabolism and glycine degradation / pyruvate dehydrogenase (NAD+) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / : / identical protein binding
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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
Acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu, S. / Xia, X. / Zhen, J. / Li, Z.H. / Zhou, Z.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI060567 United States
CitationJournal: Cell Discov / Year: 2022
Title: Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney.
Authors: Shiheng Liu / Xian Xia / James Zhen / Zihang Li / Z Hong Zhou /
Abstract: The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members ...The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
History
DepositionApr 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
01: Acetyltransferase component of pyruvate dehydrogenase complex
02: Acetyltransferase component of pyruvate dehydrogenase complex
03: Acetyltransferase component of pyruvate dehydrogenase complex
04: Acetyltransferase component of pyruvate dehydrogenase complex
05: Acetyltransferase component of pyruvate dehydrogenase complex
0z: Acetyltransferase component of pyruvate dehydrogenase complex
1a: Acetyltransferase component of pyruvate dehydrogenase complex
1b: Acetyltransferase component of pyruvate dehydrogenase complex
1c: Acetyltransferase component of pyruvate dehydrogenase complex
1d: Acetyltransferase component of pyruvate dehydrogenase complex
1e: Acetyltransferase component of pyruvate dehydrogenase complex
1f: Acetyltransferase component of pyruvate dehydrogenase complex
1g: Acetyltransferase component of pyruvate dehydrogenase complex
1h: Acetyltransferase component of pyruvate dehydrogenase complex
1i: Acetyltransferase component of pyruvate dehydrogenase complex
1j: Acetyltransferase component of pyruvate dehydrogenase complex
1k: Acetyltransferase component of pyruvate dehydrogenase complex
1l: Acetyltransferase component of pyruvate dehydrogenase complex
1m: Acetyltransferase component of pyruvate dehydrogenase complex
1n: Acetyltransferase component of pyruvate dehydrogenase complex
1o: Acetyltransferase component of pyruvate dehydrogenase complex
1p: Acetyltransferase component of pyruvate dehydrogenase complex
1q: Acetyltransferase component of pyruvate dehydrogenase complex
1r: Acetyltransferase component of pyruvate dehydrogenase complex
1s: Acetyltransferase component of pyruvate dehydrogenase complex
1t: Acetyltransferase component of pyruvate dehydrogenase complex
1u: Acetyltransferase component of pyruvate dehydrogenase complex
1v: Acetyltransferase component of pyruvate dehydrogenase complex
1w: Acetyltransferase component of pyruvate dehydrogenase complex
1x: Acetyltransferase component of pyruvate dehydrogenase complex
1z: Acetyltransferase component of pyruvate dehydrogenase complex
2a: Acetyltransferase component of pyruvate dehydrogenase complex
2b: Acetyltransferase component of pyruvate dehydrogenase complex
2c: Acetyltransferase component of pyruvate dehydrogenase complex
2d: Acetyltransferase component of pyruvate dehydrogenase complex
2e: Acetyltransferase component of pyruvate dehydrogenase complex
2f: Acetyltransferase component of pyruvate dehydrogenase complex
2g: Acetyltransferase component of pyruvate dehydrogenase complex
2h: Acetyltransferase component of pyruvate dehydrogenase complex
2i: Acetyltransferase component of pyruvate dehydrogenase complex
2j: Acetyltransferase component of pyruvate dehydrogenase complex
2k: Acetyltransferase component of pyruvate dehydrogenase complex
2l: Acetyltransferase component of pyruvate dehydrogenase complex
2m: Acetyltransferase component of pyruvate dehydrogenase complex
2n: Acetyltransferase component of pyruvate dehydrogenase complex
2o: Acetyltransferase component of pyruvate dehydrogenase complex
2p: Acetyltransferase component of pyruvate dehydrogenase complex
2q: Acetyltransferase component of pyruvate dehydrogenase complex
2r: Acetyltransferase component of pyruvate dehydrogenase complex
2s: Acetyltransferase component of pyruvate dehydrogenase complex
2t: Acetyltransferase component of pyruvate dehydrogenase complex
2u: Acetyltransferase component of pyruvate dehydrogenase complex
2v: Acetyltransferase component of pyruvate dehydrogenase complex
2w: Acetyltransferase component of pyruvate dehydrogenase complex
2x: Acetyltransferase component of pyruvate dehydrogenase complex
2y: Acetyltransferase component of pyruvate dehydrogenase complex
2z: Acetyltransferase component of pyruvate dehydrogenase complex
3a: Acetyltransferase component of pyruvate dehydrogenase complex
3b: Acetyltransferase component of pyruvate dehydrogenase complex
3c: Acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)4,148,55660
Polymers4,148,55660
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Acetyltransferase component of pyruvate dehydrogenase complex


Mass: 69142.594 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: kidney / Tissue: kidney
References: UniProt: F1N690, dihydrolipoyllysine-residue acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.069 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (cattle) / Cellular location: mitochondrial matrix / Organ: kidney / Organelle: mitochondria / Tissue: kidney
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
4CTFFINDCTF correction
7UCSF ChimeraXmodel fitting
12RELION33D reconstruction
13Cootmodel refinement
14ISOLDEmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33138 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Atomic model buildingPDB-ID: 6CT0

6ct0


Accession code: 6CT0 / Source name: PDB / Type: experimental model

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