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Basic information

Entry
Database: PDB / ID: 4qoy
TitleNovel binding motif and new flexibility revealed by structural analysis of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase sub-complex from the escherichia coli pyruvate dehydrogenase multi-enzyme complex
Components
  • Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)
  • Pyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / PSBD / PYRUVATE DEHYDROGENASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / glycolytic process
Similarity search - Function
Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / E3-binding domain / Dihydrolipoamide Transferase / 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. / Rossmann fold - #920 ...Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / E3-binding domain / Dihydrolipoamide Transferase / 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. / Rossmann fold - #920 / 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 / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Chloramphenicol acetyltransferase-like domain superfamily / Few Secondary Structures / Irregular / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsFurey, W. / Arjunan, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Novel Binding Motif and New Flexibility Revealed by Structural Analyses of a Pyruvate Dehydrogenase-Dihydrolipoyl Acetyltransferase Subcomplex from the Escherichia coli Pyruvate Dehydrogenase Multienzyme Complex.
Authors: Arjunan, P. / Wang, J. / Nemeria, N.S. / Reynolds, S. / Brown, I. / Chandrasekhar, K. / Calero, G. / Jordan, F. / Furey, W.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
C: Pyruvate dehydrogenase E1 component
D: Pyruvate dehydrogenase E1 component
E: Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)
F: Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)


Theoretical massNumber of molelcules
Total (without water)409,0276
Polymers409,0276
Non-polymers00
Water23,2931293
1
A: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
E: Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)


Theoretical massNumber of molelcules
Total (without water)204,5143
Polymers204,5143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Pyruvate dehydrogenase E1 component
D: Pyruvate dehydrogenase E1 component
F: Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)


Theoretical massNumber of molelcules
Total (without water)204,5143
Polymers204,5143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.940, 326.840, 77.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Pyruvate dehydrogenase E1 component


Mass: 99657.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 TW14359 / EHEC / Gene: aceE, B0114, ECS0118, ECSP_0115, Z0124 / Plasmid: JRG PGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456
References: UniProt: C6UVU8, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein/peptide Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component) / Pyruvate dehydrogenase dihydrolipoyltransacetylase component


Mass: 5199.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: aceF, ECs0119, Z0125 / Plasmid: JRG PGS501 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 1342 / References: UniProt: Q8X966
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1293 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 20% PEG3350 0.2M AMMONIUM TARTRATE DIBASIC,SODIUM AZIDE, PH 6.35, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.8→32.29 Å / Num. all: 132370 / Num. obs: 132035 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.32 % / Biso Wilson estimate: 82.01 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.5 / Num. unique all: 13058 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
d*TREKdata reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
SERGUIdata collection
d*TREKdata scaling
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2IEA

2iea


Resolution: 2.8→32.29 Å / Cor.coef. Fo:Fc: 0.9471 / Cor.coef. Fo:Fc free: 0.9247 / SU R Cruickshank DPI: 1.068 / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 6292 5.04 %RANDOM
Rwork0.1982 ---
obs0.1999 124907 94.36 %-
all-132370 --
Displacement parametersBiso max: 205.77 Å2 / Biso mean: 80.53 Å2 / Biso min: 28.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.9855 Å20 Å20 Å2
2--0.7342 Å20 Å2
3---0.2514 Å2
Refine analyzeLuzzati coordinate error obs: 0.447 Å
Refinement stepCycle: LAST / Resolution: 2.8→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27874 0 0 1293 29167
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_dihedral_angle_d15.1413214SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0.006784HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.0144137HARMONIC5
X-RAY DIFFRACTIONt_it5.528485HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion0.0793608SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2.08933577SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d0.00928485HARMONIC2
X-RAY DIFFRACTIONt_angle_deg138490HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion3.15
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3605 407 5.02 %
Rwork0.3522 7696 -
all0.3526 8103 -
obs--94.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3127-0.48170.26451.55-0.54230.4395-0.01830.17830.2005-0.1033-0.0842-0.2243-0.01060.04830.1025-0.1251-0.0937-0.0646-0.10630.0692-0.143326.334950.5497-5.0977
21.09460.4560.48552.1962-0.52680.6478-0.0295-0.25340.0650.4377-0.1122-0.3302-0.26170.23110.1417-0.0722-0.0108-0.152-0.00580.0293-0.104236.090825.173723.5127
31.07810.2538-0.10491.1699-0.32311.5705-0.0406-0.1383-0.26970.1131-0.0972-0.38950.12830.29450.1378-0.09960.0898-0.0932-0.05740.0709-0.001734.9367-1.701318.9213
40.7708-0.3874-0.33921.14760.21610.6219-0.0744-0.16480.1720.28130.0383-0.0709-0.16180.05680.0361-0.02260.0317-0.0882-0.0848-0.0036-0.19360.37335.039525.4023
52.0391-0.1235-0.20911.00370.55251.2176-0.04120.28910.1248-0.28890.0111-0.0325-0.0507-0.06090.03010.0130.0136-0.0383-0.03640.0485-0.180213.326816.7263-7.1394
60.90850.09510.18540.8914-0.15130.8521-0.07240.2166-0.2053-0.2643-0.0059-0.39760.17390.28560.0783-0.0440.06840.0868-0.03340.0227-0.020436.13991.1478-6.2372
71.6080.4224-0.16571.8843-0.92051.0652-0.06990.0294-0.2467-0.28490.16330.12240.1716-0.1707-0.0934-0.2207-0.152-0.1029-0.20080.103-0.14543.336779.407950.0057
81.2919-0.7392-0.44772.153-0.8962.0755-0.00380.09130.54420.01030.25720.5442-0.3293-0.2391-0.2535-0.2389-0.0464-0.0984-0.28270.1520.194636.7855117.98341.7767
92.7555-1.03111.63960.5171-2.91042.5288-0.01170.23040.2253-0.09010.02810.1736-0.317-0.2981-0.0164-0.2834-0.0989-0.152-0.26750.152-0.01632.4414125.8816.0459
102.81141.3140.26381.973-0.57241.06280.0028-0.08490.1625-0.04240.02970.1304-0.15840.0349-0.0324-0.1256-0.1390.0276-0.262-0.0185-0.282673.2133108.77541.4924
112.29061.83541.08320.88260.29122.0663-0.0760.5442-0.394-0.54150.29760.08320.1689-0.0557-0.2216-0.0133-0.152-0.152-0.0656-0.0101-0.303748.649491.378815.9469
123.13290.69342.41470.5971-1.18543.58360.05090.4363-0.0789-0.1238-0.00980.1336-0.0976-0.2991-0.0411-0.2949-0.152-0.1520.04420.152-0.30424.9299102.6878.9323
130-0.93790.87590.8028-0.27870.00110.00060.00590.03310.04160.0044-0.04240.0102-0.0524-0.005-0.14860.0263-0.0209-0.09380.02360.0086-2.174783.01850.9719
140.26970.18440.54910-1.00960.02130.00230.0017-0.02320.0491-0.00480.0411-0.0107-0.03180.0025-0.21060.0130.019-0.03210.1103-0.051985.763280.25479.3962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|470 }A5 - 470
2X-RAY DIFFRACTION2{ A|471 - A|705 }A471 - 705
3X-RAY DIFFRACTION3{ A|706 - A|886 }A706 - 886
4X-RAY DIFFRACTION4{ B|5 - B|470 }B5 - 470
5X-RAY DIFFRACTION5{ B|471 - B|705 }B471 - 705
6X-RAY DIFFRACTION6{ B|706 - B|886 }B706 - 886
7X-RAY DIFFRACTION7{ C|5 - C|470 }C5 - 470
8X-RAY DIFFRACTION8{ C|471 - C|705 }C471 - 705
9X-RAY DIFFRACTION9{ C|706 - C|886 }C706 - 886
10X-RAY DIFFRACTION10{ D|7 - D|470 }D7 - 470
11X-RAY DIFFRACTION11{ D|471 - D|705 }D471 - 705
12X-RAY DIFFRACTION12{ D|706 - D|886 }D706 - 886
13X-RAY DIFFRACTION13{ E|122 - E|167 }E122 - 167
14X-RAY DIFFRACTION14{ F|122 - F|167 }F122 - 167

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