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- PDB-2pnr: Crystal Structure of the asymmetric Pdk3-l2 Complex -

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Basic information

Entry
Database: PDB / ID: 2pnr
TitleCrystal Structure of the asymmetric Pdk3-l2 Complex
Components
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
  • [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
KeywordsTRANSFERASE / pyruvate dehydrogenase kinase 3 / lipoyl-bearing domain / asymmetric protein-protein complex
Function / homology
Function and homology information


hypoxia-inducible factor-1alpha signaling pathway / PDH complex synthesizes acetyl-CoA from PYR / [pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate catabolic process / Protein lipoylation ...hypoxia-inducible factor-1alpha signaling pathway / PDH complex synthesizes acetyl-CoA from PYR / [pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate catabolic process / Protein lipoylation / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / cellular response to fatty acid / Signaling by Retinoic Acid / regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / tricarboxylic acid cycle / peroxisome proliferator activated receptor signaling pathway / cellular response to glucose stimulus / peptidyl-serine phosphorylation / glucose metabolic process / protein kinase activity / mitochondrial matrix / protein serine/threonine kinase activity / nucleolus / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / 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) / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Chloramphenicol acetyltransferase-like domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIHYDROLIPOIC ACID / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVassylyev, D.G. / Steussy, C.N. / Devedjiev, Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of an Asymmetric complex of Pyruvate Dehydrogenase Kinase 3 with Lipoyl domain 2 and its Biological Implications
Authors: Devedjiev, Y. / Steussy, C.N. / Vassylyev, D.G.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
B: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
E: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
F: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
G: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,9658
Polymers221,5486
Non-polymers4172
Water13,025723
1
A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
B: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9824
Polymers110,7743
Non-polymers2081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
F: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
G: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9824
Polymers110,7743
Non-polymers2081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.155, 96.155, 222.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 / Pyruvate dehydrogenase kinase isoform 3


Mass: 48290.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK3 / Plasmid: PTRCHISB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q15120, [pyruvate dehydrogenase (acetyl-transferring)] kinase
#2: Protein Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase complex E2 subunit / PDCE2 / E2 / Dihydrolipoamide S-acetyltransferase ...Pyruvate dehydrogenase complex E2 subunit / PDCE2 / E2 / Dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex / PDC-E2 / 70 kDa mitochondrial autoantigen of primary biliary cirrhosis / PBC / M2 antigen complex 70 kDa subunit


Mass: 14192.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLAT, DLTA / Plasmid: PTRCHISB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase
#3: Chemical ChemComp-RED / DIHYDROLIPOIC ACID


Mass: 208.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein solution: 5mg/ml, 20mM Tris-HCL pH 8.0, 100mM NaCl, 5mM DTT, 2.5% (v/v) ethylen glycol Precipitant solution: 100mM histidine, 30 mM EDTA, 7% (v/v) MPD., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2002
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 64645 / Num. obs: 64645 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4439 / Rsym value: 0.422 / % possible all: 64

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8N

1y8n


Resolution: 2.5→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED ...Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED OUT USING THE TWINNING OPTION OF THE CNS PROGRAM. FOR THE DEPOSITION THE DIFFRACTION DATA WERE DETWINNED USING THE CNS PROGRAM. THE REFINEMENT STATISTICS CALCULATED BASED ON THE DETWINNED DATA MIGHT BE SLIGHTLY DIFFERENT FROM THOSE OBTAINED DURING THE "TWINNED" REFINEMENT INCLUDED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3746 -random
Rwork0.176 ---
all0.185 64645 --
obs0.185 64645 92.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12858 0 22 723 13603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_improper_angle_d0.842
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.306 286 -
Rwork0.279 --
obs-4439 64 %

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