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- PDB-9h2i: Dihydrolipoyl Dehydrogenase (E3) in complex with the binding doma... -

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Basic information

Entry
Database: PDB / ID: 9h2i
TitleDihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate dehydrogenase complex
Components
  • Dihydrolipoyl dehydrogenase
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
KeywordsFLAVOPROTEIN / complex / pyruvate dehydrogenase / electrostatic binding
Function / homology
Function and homology information


glycine decarboxylation via glycine cleavage system / glycine cleavage complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / pyruvate catabolic process / oxoglutarate dehydrogenase complex / pyruvate decarboxylation to acetyl-CoA ...glycine decarboxylation via glycine cleavage system / glycine cleavage complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / pyruvate catabolic process / oxoglutarate dehydrogenase complex / pyruvate decarboxylation to acetyl-CoA / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / 2-oxoglutarate metabolic process / pyruvate metabolic process / acetyltransferase activity / tricarboxylic acid cycle / one-carbon metabolic process / flavin adenine dinucleotide binding / response to oxidative stress / zinc ion binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Dihydrolipoamide dehydrogenase / : / : / 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. ...Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Dihydrolipoamide dehydrogenase / : / : / 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) / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme / FAD/NAD-linked reductase, dimerisation domain superfamily / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBothe, S.N. / Zajec Hudnik, T. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: A cooperative binding mechanism steers the recruitment of peripheral subunits in the E. coli pyruvate dehydrogenase complex
Authors: Bothe, S.N. / Racunica, D. / Zajec Hudnik, T. / Zdanowicz, R. / Bothe, A. / Giese, C. / Glockshuber, R.
History
DepositionOct 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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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: Dihydrolipoyl dehydrogenase
C: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0305
Polymers108,4593
Non-polymers1,5712
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-65 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.703, 88.353, 200.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 7210.218 Da / Num. of mol.: 1
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: Protein Dihydrolipoyl dehydrogenase / Dihydrolipoamide dehydrogenase / E3 component of pyruvate and 2-oxoglutarate dehydrogenases ...Dihydrolipoamide dehydrogenase / E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes / Glycine cleavage system L protein


Mass: 50624.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpdA, lpd, b0116, JW0112 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A9P0, dihydrolipoyl dehydrogenase
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 18% w/v PEG 3350, 200 mM disodium malonate, pH 4.0 1 uL reservoir + 2 uL 11.4 mg/mL E3:PSBD complex

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.97→100.3 Å / Num. obs: 77255 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 12.8
Reflection shellResolution: 1.97→2 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3810 / CC1/2: 0.778 / Rpim(I) all: 0.3 / Rrim(I) all: 1.13 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→36.86 Å / SU ML: 0.2166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 3904 5.06 %
Rwork0.1898 73266 -
obs0.1919 77170 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.55 Å2
Refinement stepCycle: LAST / Resolution: 1.97→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7459 0 106 581 8146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747706
X-RAY DIFFRACTIONf_angle_d0.913410448
X-RAY DIFFRACTIONf_chiral_restr0.05811199
X-RAY DIFFRACTIONf_plane_restr0.00661334
X-RAY DIFFRACTIONf_dihedral_angle_d15.60362806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.31681270.27172571X-RAY DIFFRACTION100
1.99-2.020.32831490.25012606X-RAY DIFFRACTION100
2.02-2.050.26571380.23962557X-RAY DIFFRACTION100
2.05-2.070.30711450.23832587X-RAY DIFFRACTION100
2.07-2.10.28381310.23432614X-RAY DIFFRACTION100
2.1-2.130.26651480.22662525X-RAY DIFFRACTION100
2.13-2.170.27261460.22222619X-RAY DIFFRACTION100
2.17-2.20.28131410.21532573X-RAY DIFFRACTION100
2.2-2.240.25031500.222591X-RAY DIFFRACTION100
2.24-2.280.26771470.22732603X-RAY DIFFRACTION100
2.28-2.330.28761260.21962612X-RAY DIFFRACTION100
2.33-2.370.29641350.21542557X-RAY DIFFRACTION99.96
2.37-2.430.27711440.20932617X-RAY DIFFRACTION99.93
2.43-2.480.21781380.20792563X-RAY DIFFRACTION99.93
2.48-2.540.2631370.19912634X-RAY DIFFRACTION100
2.54-2.610.25881240.20162630X-RAY DIFFRACTION100
2.61-2.690.23471330.1992574X-RAY DIFFRACTION99.41
2.69-2.780.23121400.20142607X-RAY DIFFRACTION99.21
2.78-2.870.27191470.21612595X-RAY DIFFRACTION99.93
2.88-2.990.28371280.22272620X-RAY DIFFRACTION99.96
2.99-3.130.24231210.20482642X-RAY DIFFRACTION99.96
3.13-3.290.26931290.20552632X-RAY DIFFRACTION99.89
3.29-3.50.23351430.19482633X-RAY DIFFRACTION99.71
3.5-3.770.22541440.18092647X-RAY DIFFRACTION99.79
3.77-4.150.20481500.16942645X-RAY DIFFRACTION99.82
4.15-4.740.17431440.14782675X-RAY DIFFRACTION100
4.74-5.970.20861390.17182721X-RAY DIFFRACTION99.58
5.97-36.860.20051600.17012816X-RAY DIFFRACTION99.5

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