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- PDB-3dva: Snapshots of catalysis in the E1 subunit of the pyruvate dehydrog... -

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Basic information

Entry
Database: PDB / ID: 3dva
TitleSnapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Components
  • (Pyruvate dehydrogenase E1 component subunit ...) x 2
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complexDihydrolipoyl transacetylase
KeywordsOXIDOREDUCTASE/TRANSFERASE / Oxidoreductase / PYRUVATE / DEHYDROGENASE / DIHYDROLIPOYL / ACETYL TRANSFERASE / MULTIENZYME COMPLEX / TRANSFERASE / Glycolysis / Phosphoprotein / Thiamine pyrophosphate / Acyltransferase / OXIDOREDUCTASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / glycolytic process / cytoplasm
Similarity search - Function
Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha / E3-binding domain / Dihydrolipoamide Transferase / Dehydrogenase, E1 component / Dehydrogenase E1 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 ...Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha / E3-binding domain / Dihydrolipoamide Transferase / Dehydrogenase, E1 component / Dehydrogenase E1 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. / Transketolase, C-terminal domain / Transketolase, C-terminal domain / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / 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 / Thiamin diphosphate-binding fold / Few Secondary Structures / Irregular / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-TPW / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase E1 component subunit alpha / Pyruvate dehydrogenase E1 component subunit beta
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPei, X.Y. / Titman, C.M. / Frank, R.A.W. / Leeper, F.J. / Luisi, B.F.
CitationJournal: Structure / Year: 2008
Title: Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex
Authors: Pei, X.Y. / Titman, C.M. / Frank, R.A. / Leeper, F.J. / Luisi, B.F.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component subunit alpha
B: Pyruvate dehydrogenase E1 component subunit beta
C: Pyruvate dehydrogenase E1 component subunit alpha
D: Pyruvate dehydrogenase E1 component subunit beta
E: Pyruvate dehydrogenase E1 component subunit alpha
F: Pyruvate dehydrogenase E1 component subunit beta
G: Pyruvate dehydrogenase E1 component subunit alpha
H: Pyruvate dehydrogenase E1 component subunit beta
I: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
J: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,58922
Polymers400,67110
Non-polymers1,91712
Water20,3031127
1
A: Pyruvate dehydrogenase E1 component subunit alpha
B: Pyruvate dehydrogenase E1 component subunit beta
C: Pyruvate dehydrogenase E1 component subunit alpha
D: Pyruvate dehydrogenase E1 component subunit beta
I: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,33312
Polymers200,3365
Non-polymers9987
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23740 Å2
ΔGint-130.1 kcal/mol
Surface area44440 Å2
MethodPISA
2
E: Pyruvate dehydrogenase E1 component subunit alpha
F: Pyruvate dehydrogenase E1 component subunit beta
G: Pyruvate dehydrogenase E1 component subunit alpha
H: Pyruvate dehydrogenase E1 component subunit beta
J: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,25510
Polymers200,3365
Non-polymers9205
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23290 Å2
ΔGint-142.5 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.673, 232.294, 91.936
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Pyruvate dehydrogenase E1 component subunit ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Pyruvate dehydrogenase E1 component subunit alpha


Mass: 41476.094 Da / Num. of mol.: 4 / Mutation: I206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pdhA / Plasmid: pKBstE1a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 recO
References: UniProt: P21873, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein
Pyruvate dehydrogenase E1 component subunit beta


Mass: 35495.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pdhB / Plasmid: pKBstE1b / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 recO
References: UniProt: P21874, pyruvate dehydrogenase (acetyl-transferring)

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Protein , 1 types, 2 molecules IJ

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


Mass: 46392.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pdhC / Plasmid: pKBstE1a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 recO
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase

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Non-polymers , 4 types, 1139 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-TPW / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / 3-DEAZA-THDP


Mass: 423.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H19N3O7P2S
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1127 / 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: 1.83 Å3/Da / Density % sol: 32.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR ...Details: The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.35→77 Å / Num. obs: 117919 / % possible obs: 98.9 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Rsym value: 0.091 / Net I/σ(I): 13.9
Reflection shellResolution: 2.35→2.46 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.265 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1w85

1w85


Resolution: 2.35→72.17 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.885 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24718 5906 5 %RANDOM
Rwork0.1896 ---
obs0.19248 111973 98.9 %-
all-111973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.681 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20.25 Å2
2---0.93 Å20 Å2
3----1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.271 Å0.196 Å
Luzzati d res low-2.35 Å
Luzzati sigma a0.267 Å0.263 Å
Refinement stepCycle: LAST / Resolution: 2.35→72.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22043 0 115 1127 23285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02222681
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.141.97430697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.50352828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56424.5411057
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.493153912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.30115149
X-RAY DIFFRACTIONr_chiral_restr0.170.23381
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217299
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.312629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.515993
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.52461
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.511
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4080.3125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4480.544
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2110.510
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.686214101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.953322701
X-RAY DIFFRACTIONr_scbond_it0.34128580
X-RAY DIFFRACTIONr_scangle_it0.56937996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 353 -
Rwork0.217 7326 -
obs--87.52 %

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