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- PDB-2ozl: Human pyruvate dehydrogenase S264E variant -

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Basic information

Entry
Database: PDB / ID: 2ozl
TitleHuman pyruvate dehydrogenase S264E variant
Components(Pyruvate dehydrogenase E1 component ...) x 2
KeywordsOXIDOREDUCTASE / pyruvate_dehydrogenase_complex / human / E1 / multienzyme_complex_component / thiamine_pyrophosphate / thiamin_diphosphate / heterotetrameric / lipoyl_substrate / pyruvate / dihydrolipoamide_acetyltransferase / dihydrolipoamide_dehydrogenase
Function / homology
Function and homology information


: / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / PDH complex synthesizes acetyl-CoA from PYR / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / Mitochondrial protein degradation ...: / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / PDH complex synthesizes acetyl-CoA from PYR / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / Mitochondrial protein degradation / glucose metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal 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 / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIAMINE DIPHOSPHATE / Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCiszak, E.M. / Dominiak, P.M. / Patel, M.S. / Korotchkina, L.G.
CitationJournal: Biochemistry / Year: 2007
Title: Phosphorylation of Serine 264 Impedes Active Site Accessibility in the E1 Component of the Human Pyruvate Dehydrogenase Multienzyme Complex
Authors: Seifert, F. / Ciszak, E.M. / Korotchkina, L.G. / Golbik, R. / Spinka, M. / Dominiak, P.M. / Sidhu, S. / Brauer, J. / Patel, M.S. / Tittmann, K.
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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 alpha subunit, somatic form
B: Pyruvate dehydrogenase E1 component subunit beta
C: Pyruvate dehydrogenase E1 component alpha subunit, somatic form
D: Pyruvate dehydrogenase E1 component subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,18410
Polymers156,2074
Non-polymers9776
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22260 Å2
ΔGint-148 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.9, 126.4, 190.4
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly consists of two alpha subunits and two beta subunits (alpha2,beta2-heterotetramer)

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Components

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Pyruvate dehydrogenase E1 component ... , 2 types, 4 molecules ACBD

#1: Protein Pyruvate dehydrogenase E1 component alpha subunit, somatic form / E.C.1.2.4.1 / PDHE1-A type I


Mass: 40756.523 Da / Num. of mol.: 2 / Fragment: Alpha subunit / Mutation: S264E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHA1, PHE1A / Plasmid: pET21 / Production host: Escherichia coli (E. coli)
References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein Pyruvate dehydrogenase E1 component subunit beta / E.C.1.2.4.1 / PDHE1-B


Mass: 37346.836 Da / Num. of mol.: 2 / Fragment: Beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHB, PHE1B / Plasmid: pET21 / Production host: Escherichia coli (E. coli)
References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring)

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Non-polymers , 4 types, 763 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14-18% PEG3350, 100-200mM NaSCN, 5mM DTT, 0.1mM NaN3,, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.2 Å
DetectorDetector: CCD / Date: Jun 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 111312 / Num. obs: 106472 / % possible obs: 91.1 % / Redundancy: 3.23 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 5.56

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NI4

1ni4


Resolution: 1.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 10657 -random
Rwork0.186 ---
all0.1861 111312 --
obs0.1861 106472 85.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10704 0 56 757 11517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.27

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