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

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Basic information

Entry
Database: PDB / ID: 8egu
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 / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / regulation of glucose metabolic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / 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-U35 / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.923 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)45,6565
Polymers44,2621
Non-polymers1,3944
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.159, 111.159, 141.744
Angle α, β, γ (deg.)90, 90, 120
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 / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-U35 / (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid / (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid / Diovan / Tareg / Provas / Exforge / N-(p-(o-1H-Tetrazol-5-ylphenyl)benzyl)-N-valeryl-L-valine / Valsartan


Mass: 435.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N5O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium citrate pH 5.6, 800 mM lithium sulfate, and 750 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 16M / 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: 1.923→96.267 Å / Num. obs: 29906 / % possible obs: 87.1 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.019 / Net I/σ(I): 18.5
Reflection shellResolution: 1.923→2.101 Å / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1494 / CC1/2: 0.757 / Rpim(I) all: 0.338 / % possible all: 42

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 40 / Resolution: 1.923→96.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 1564 -RANDOM
Rwork0.2379 ---
obs0.2395 29906 75 %-
Displacement parametersBiso mean: 52.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.858 Å20 Å20 Å2
2--0.858 Å20 Å2
3----1.7159 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.923→96.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 96 160 2849
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082817HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.883865HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d981SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it2763HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion351SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2305SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 1.923→2.02 Å
RfactorNum. reflection% reflection
Rfree0.373 30 -
Rwork0.2627 --
obs--11.17 %
Refinement TLS params.Origin x: 101.6782 Å / Origin y: 35.9381 Å / Origin z: 22.4393 Å
111213212223313233
T-0.0521 Å20.0664 Å2-0.0125 Å2-0.1366 Å2-0.0057 Å2---0.0414 Å2
L0.4877 °20.0027 °20.7536 °2-0.1631 °2-0.8486 °2--2.9422 °2
S0.1499 Å °-0.075 Å °0.3072 Å °-0.075 Å °-0.2017 Å °0.6366 Å °0.3072 Å °0.6366 Å °0.0518 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A25 - 374
2X-RAY DIFFRACTION1{ A|* }A401 - 403

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