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- PDB-1jm6: Pyruvate dehydrogenase kinase, isozyme 2, containing ADP -

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Basic information

Entry
Database: PDB / ID: 1jm6
TitlePyruvate dehydrogenase kinase, isozyme 2, containing ADP
ComponentsPyruvate dehydrogenase kinase, isozyme 2
KeywordsTRANSFERASE / Kinase / Mitochondion / Serine Kinase
Function / homology
Function and homology information


Signaling by Retinoic Acid / Regulation of pyruvate dehydrogenase (PDH) complex / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / pyruvate dehydrogenase complex / : / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient ...Signaling by Retinoic Acid / Regulation of pyruvate dehydrogenase (PDH) complex / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / pyruvate dehydrogenase complex / : / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / cellular response to reactive oxygen species / glucose homeostasis / insulin receptor signaling pathway / peptidyl-serine phosphorylation / protein serine/threonine kinase activity / protein-containing complex binding / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 ...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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / 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 / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 2.5 Å
AuthorsSteussy, C.N. / Popov, K.M. / Bowker-Kinley, M.M. / Sloan, R.B. / Harris, R.A. / Hamilton, J.A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure of pyruvate dehydrogenase kinase. Novel folding pattern for a serine protein kinase.
Authors: Steussy, C.N. / Popov, K.M. / Bowker-Kinley, M.M. / Sloan Jr., R.B. / Harris, R.A. / Hamilton, J.A.
History
DepositionJul 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase kinase, isozyme 2
B: Pyruvate dehydrogenase kinase, isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2146
Polymers92,3112
Non-polymers9034
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-49 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.421, 109.874, 71.414
Angle α, β, γ (deg.)90.00, 104.52, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological dimer is recreated using a crystallographically equivalent position of the B subunit. This can be achieved by applying the following translation vector to the B coordinates; 17.90 -109.87 -69.13

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Components

#1: Protein Pyruvate dehydrogenase kinase, isozyme 2 / / E.C.2.7.1.99 / [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2 / MITOCHONDRIAL / PDK P45


Mass: 46155.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: Pet28a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q64536, EC: 2.7.1.99
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.95 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 6k, Imidazole, ADP, Magnesium Chloride, Iodo-propionic Acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMimidazole1reservoiror 100mM MES
3500 mM1reservoirKCl
43.5 mM3-iodopropionic acid1reservoir
53.5 mMADP1reservoir
67 mM1reservoirMgCl2
76.5 %PEG60001reservoir
81.0 %ethylene glycol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONNSLS X12C20.9803, 0.9802, 0.9300
Detector
TypeIDDetectorDate
RIGAKU RAXIS II1IMAGE PLATEApr 1, 1999
CUSTOM-MADE2CCDMar 26, 1998
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteSINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.98031
30.98021
40.931
ReflectionResolution: 2.4→20 Å / Num. all: 36213 / Num. obs: 35685 / % possible obs: 88.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 23.1
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 76.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.287

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 2.5→6 Å / Num. parameters: 22712 / Num. restraintsaints: 29468 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 1508 5.2 %RANDOM
Rwork0.202 ---
all0.1905 28853 --
obs0.208 28853 84.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5677
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5393 0 56 228 5677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0.316
X-RAY DIFFRACTIONs_from_restr_planes0.019
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.139
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.4

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