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- PDB-1w85: The crystal structure of pyruvate dehydrogenase E1 bound to the p... -

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Basic information

Entry
Database: PDB / ID: 1w85
TitleThe crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
Components
  • (PYRUVATE DEHYDROGENASE E1 COMPONENT, ...) x 2
  • DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATEDihydrolipoyl transacetylase
KeywordsOXIDOREDUCTASE / PYRUVATE / DEHYDROGENASE / DIHYDROLIPOYL / ACETYL TRANSFERASE / MULTIENZYME COMPLEX / TRANSFERASE
Function / homology
Function and homology information


pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / 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 / Rossmann fold - #920 / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / 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
: / DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase E1 component subunit alpha / Pyruvate dehydrogenase E1 component subunit beta
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFrank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F.
Citation
Journal: Science / Year: 2004
Title: A molecular switch and proton wire synchronize the active sites in thiamine enzymes.
Authors: Frank, R.A. / Titman, C.M. / Pratap, J.V. / Luisi, B.F. / Perham, R.N.
#1: Journal: To be Published
Title: Molecular Assembly of a Multi-Enzymes Complex: The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2
Authors: Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F.
History
DepositionSep 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 8, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation / Other
Category: atom_site / citation ...atom_site / citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 3.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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_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_conn.ptnr2_label_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.1Dec 13, 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, ALPHA SUBUNIT
B: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
C: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
D: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
E: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
F: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
G: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
H: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
I: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
J: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,85227
Polymers317,53010
Non-polymers2,32217
Water31,2201733
1
A: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
B: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
C: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
D: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
I: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,97914
Polymers158,7655
Non-polymers1,2149
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
F: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
G: PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT
H: PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT
J: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,87313
Polymers158,7655
Non-polymers1,1088
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.270, 232.330, 91.924
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.975356, -0.219264, -0.024566), (0.218899, -0.975605, 0.016697), (-0.027627, 0.010908, 0.999559)
Vector: 74.56577, 177.63184, 45.67485)
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

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PYRUVATE DEHYDROGENASE E1 COMPONENT, ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT


Mass: 41386.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P21873, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein
PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT


Mass: 35364.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P21874, pyruvate dehydrogenase (acetyl-transferring)

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Protein/peptide , 1 types, 2 molecules IJ

#3: Protein/peptide DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE / Dihydrolipoyl transacetylase / E2 / DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX


Mass: 5262.105 Da / Num. of mol.: 2
Fragment: PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 122-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase

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Non-polymers , 5 types, 1750 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1733 / 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: 2.21 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD / Date: May 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 171898 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 68.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QS0

1qs0


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FOLLOWING TERMINAL RESIDUES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY MAP AND ARE NOT MODELLED: A1-A3, A368, C1-C3, E1-E4, G1-G4, I122-I127, I170, J122-J128, J167-J170. IN ...Details: THE FOLLOWING TERMINAL RESIDUES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY MAP AND ARE NOT MODELLED: A1-A3, A368, C1-C3, E1-E4, G1-G4, I122-I127, I170, J122-J128, J167-J170. IN ADDITION, THE FOLLOWING RESIDUES COULD NOT BE MODELLED: A277-A282, E204-E211, E278- E283, J147-J150.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 9031 5 %RANDOM
Rwork0.176 ---
obs0.178 171898 94.8 %-
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: 21.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å2-0.32 Å2
2---0.46 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21642 0 135 1733 23510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222195
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.97430065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53252795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77324.5411002
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.833153718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.55115136
X-RAY DIFFRACTIONr_chiral_restr0.1380.23335
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0216945
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.211581
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.215416
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.21876
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.408513951
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.645622390
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39358244
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5877.57675
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 433 -
Rwork0.228 8728 -
obs--65.52 %

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