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- PDB-8oqj: Peripheral subunit binding domain of the E. coli Dihydrolipoamide... -

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Basic information

Entry
Database: PDB / ID: 8oqj
TitlePeripheral subunit binding domain of the E. coli Dihydrolipoamide Acetyltransferase (E2) of the pyruvate dehydrogenase complex
ComponentsDihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complexDihydrolipoyl transacetylase
KeywordsPROTEIN BINDING / Pyruvate dehydrogenase complex / Binding domain / Dimer / PSBD
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMeinhold, S. / Zdanowicz, R. / Glockshuber, R.
Funding support Switzerland, 1items
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 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7483
Polymers14,6832
Non-polymers651
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-26 kcal/mol
Surface area6970 Å2
Unit cell
Length a, b, c (Å)33.576, 37.831, 37.834
Angle α, β, γ (deg.)100.390, 114.386, 101.179
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoyl transacetylase / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / E2


Mass: 7341.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceF, b0115, JW0111 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06959, dihydrolipoyllysine-residue acetyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM NaOAc pH 5.0, 2 mM ZnCl2, 24 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999874 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999874 Å / Relative weight: 1
ReflectionResolution: 1.64→35.5 Å / Num. obs: 18881 / % possible obs: 96.34 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.11 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Net I/σ(I): 10.8
Reflection shellResolution: 1.64→1.7 Å / Num. unique obs: 1783 / Rpim(I) all: 0.742 / % possible all: 90.46

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→35.5 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.0573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 944 5.01 %
Rwork0.2152 17896 -
obs0.2167 18840 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.26 Å2
Refinement stepCycle: LAST / Resolution: 1.64→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 1 173 1033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071977
X-RAY DIFFRACTIONf_angle_d0.78151317
X-RAY DIFFRACTIONf_chiral_restr0.0594140
X-RAY DIFFRACTIONf_plane_restr0.007178
X-RAY DIFFRACTIONf_dihedral_angle_d3.4667147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.720.37561290.36282422X-RAY DIFFRACTION91.17
1.72-1.830.3091330.29612542X-RAY DIFFRACTION95.81
1.83-1.970.28061360.2452571X-RAY DIFFRACTION95.79
1.97-2.170.22531340.20042542X-RAY DIFFRACTION96.47
2.17-2.490.2231360.19842579X-RAY DIFFRACTION97.24
2.49-3.130.24211370.21952617X-RAY DIFFRACTION98.04
3.13-35.50.23221390.1942623X-RAY DIFFRACTION98.43

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