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- PDB-8egq: Branched chain ketoacid dehydrogenase kinase complexes -

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Basic information

Entry
Database: PDB / ID: 8egq
TitleBranched chain ketoacid dehydrogenase kinase complexes
Components[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Branched-chain ketoacid dehydrogenase / Branched-chain ketoacid dehydrogenase kinase / inhibitors / angiotensin receptor blocker / SIGNALING PROTEIN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / : / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-leucine catabolic process / branched-chain amino acid catabolic process / lipid biosynthetic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / : / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-leucine catabolic process / branched-chain amino acid catabolic process / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding
Similarity search - Function
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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-WJK / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å
AuthorsLiu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors.
Authors: Liu, S. / Kormos, B.L. / Knafels, J.D. / Sahasrabudhe, P.V. / Rosado, A. / Sommese, R.F. / Reyes, A.R. / Ward, J. / Roth Flach, R.J. / Wang, X. / Buzon, L.M. / Reese, M.R. / Bhattacharya, S. ...Authors: Liu, S. / Kormos, B.L. / Knafels, J.D. / Sahasrabudhe, P.V. / Rosado, A. / Sommese, R.F. / Reyes, A.R. / Ward, J. / Roth Flach, R.J. / Wang, X. / Buzon, L.M. / Reese, M.R. / Bhattacharya, S.K. / Omoto, K. / Filipski, K.J.
History
DepositionSep 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Assembly

Deposited unit
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5825
Polymers44,2621
Non-polymers1,3204
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 2-fold axis of the dimer is the crystallographic 2-fold axis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.267, 111.267, 140.111
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial / Branched-chain alpha-ketoacid dehydrogenase kinase / BCKD-kinase / BCKDHKIN


Mass: 44261.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bckdk / Production host: Escherichia coli (E. coli) / Strain (production host): DL21 / Variant (production host): DE3
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-WJK / (2S)-2-ethyl-4-{[(2'M)-2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazine


Mass: 398.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM bis-tris pH 5.6-6.5, 1 M lithium sulfate, and 400-840 mM ammonium sulfate
PH range: 5.6-6.5 / Temp details: 20 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.955→96.36 Å / Num. obs: 27605 / % possible obs: 88.6 % / Redundancy: 19.5 % / Biso Wilson estimate: 49.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.014 / Net I/σ(I): 24.8
Reflection shellResolution: 1.955→2.14 Å / Rmerge(I) obs: 1.489 / Num. unique obs: 1380 / CC1/2: 0.805 / Rpim(I) all: 0.337 / % possible all: 54.4

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Processing

Software
NameVersionClassification
XDSdata reduction
BUSTER2.11.8 (24-FEB-2021)refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 40 / Resolution: 1.955→96.36 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.219 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.185
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 1443 5.23 %RANDOM
Rwork0.2291 ---
obs0.2311 27605 73.3 %-
Displacement parametersBiso max: 130.34 Å2 / Biso mean: 60.15 Å2 / Biso min: 30.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.2832 Å20 Å20 Å2
2--2.2832 Å20 Å2
3----4.5664 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 1.955→96.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 92 176 2859
Biso mean--58.79 58.84 -
Num. residues----324
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d967SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes540HARMONIC5
X-RAY DIFFRACTIONt_it2749HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion350SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2232SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2791HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3819HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.44
LS refinement shellResolution: 1.96→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3525 28 5.06 %
Rwork0.283 525 -
all0.2861 553 -
obs--8.06 %
Refinement TLS params.Method: refined / Origin x: 101.6591 Å / Origin y: 35.7453 Å / Origin z: 22.6847 Å
111213212223313233
T-0.0516 Å20.1151 Å2-0.0208 Å2-0.1707 Å2-0.0779 Å2---0.111 Å2
L0.828 °2-0.0684 °20.9291 °2-0.5317 °2-1.2737 °2--3.7867 °2
S0.2114 Å °0.1768 Å °-0.0263 Å °-0.1072 Å °-0.2008 Å °-0.0067 Å °0.3974 Å °0.89 Å °-0.0106 Å °
Refinement TLS groupSelection details: { A|* }

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