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- PDB-3tz2: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3tz2
TitleCrystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate complex
Components[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GHKL protein kinase / Allosteric kinase inhibitor / Branched-chain alpha-ketoacid / Branched-chain amino acids / Maple syrup urine disease / Diabetes and obesity / Bergerat nucleotide-binding fold / Protein kinase / 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
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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain ...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 / Signal transduction histidine kinase-related protein, C-terminal / 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
4-PHENYL-BUTANOIC ACID / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTso, S.C. / Chuang, J.L. / Gui, W.J. / Wynn, R.M. / Li, J. / Chuang, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase.
Authors: Tso, S.C. / Qi, X. / Gui, W.J. / Chuang, J.L. / Morlock, L.K. / Wallace, A.L. / Ahmed, K. / Laxman, S. / Campeau, P.M. / Lee, B.H. / Hutson, S.M. / Tu, B.P. / Williams, N.S. / Tambar, U.K. / ...Authors: Tso, S.C. / Qi, X. / Gui, W.J. / Chuang, J.L. / Morlock, L.K. / Wallace, A.L. / Ahmed, K. / Laxman, S. / Campeau, P.M. / Lee, B.H. / Hutson, S.M. / Tu, B.P. / Williams, N.S. / Tambar, U.K. / Wynn, R.M. / Chuang, D.T.
History
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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

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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)47,5382
Polymers47,3741
Non-polymers1641
Water0
1
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)95,0774
Polymers94,7482
Non-polymers3282
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area30230 Å2
Unit cell
Length a, b, c (Å)128.201, 128.201, 72.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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: 47374.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bckdk / Plasmid: pTrckHisB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GroESL
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase
#2: Chemical ChemComp-CLT / 4-PHENYL-BUTANOIC ACID / GAMMA-PHENYL-BUTYRIC ACID


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2

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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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14403 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.061 / Rsym value: 0.044 / Net I/σ(I): 26.9
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.751 / % possible all: 88.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→38.38 Å / SU ML: 0.66 / σ(F): 1.33 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1438 10.01 %
Rwork0.199 --
obs0.204 14365 98.3 %
all-14620 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.51 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.742 Å2-0 Å20 Å2
2---16.742 Å20 Å2
3---33.484 Å2
Refinement stepCycle: LAST / Resolution: 2.85→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 12 0 2442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092514
X-RAY DIFFRACTIONf_angle_d1.1473399
X-RAY DIFFRACTIONf_dihedral_angle_d13.266965
X-RAY DIFFRACTIONf_chiral_restr0.071377
X-RAY DIFFRACTIONf_plane_restr0.004438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8456-2.94730.40461300.32271164X-RAY DIFFRACTION90
2.9473-3.06530.30841350.2581223X-RAY DIFFRACTION95
3.0653-3.20470.30311420.2321273X-RAY DIFFRACTION99
3.2047-3.37360.28531420.21451285X-RAY DIFFRACTION100
3.3736-3.58480.29531450.20281300X-RAY DIFFRACTION100
3.5848-3.86140.2741450.19581304X-RAY DIFFRACTION100
3.8614-4.24950.22131450.17021303X-RAY DIFFRACTION100
4.2495-4.86340.19261470.15181323X-RAY DIFFRACTION100
4.8634-6.12330.25151490.21345X-RAY DIFFRACTION100
6.1233-38.37830.21851580.21591407X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.3858 Å / Origin y: -30.5406 Å / Origin z: 10.5099 Å
111213212223313233
T0.5333 Å20.0521 Å20.041 Å2-0.6493 Å20.1585 Å2--0.5614 Å2
L1.4673 °20.4415 °2-1.1942 °2-0.8492 °20.19 °2--0.4808 °2
S-0.0976 Å °-0.3441 Å °-0.4393 Å °0.0397 Å °-0.0928 Å °-0.1078 Å °0.1254 Å °0.1799 Å °0.0319 Å °
Refinement TLS groupSelection details: all

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