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- PDB-4h7q: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4h7q
TitleCrystal structure of branched-chain alpha-ketoacid dehydrogenase kinase in complex with alpha-ketoisocaproic acid and ADP
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-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 / 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 / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / 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
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
ADENOSINE-5'-DIPHOSPHATE / 2-OXO-4-METHYLPENTANOIC ACID / : / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Feb 28, 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_ref_seq_dif / 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_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_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_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

Downloads & links

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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)47,9955
Polymers47,3741
Non-polymers6214
Water1,31573
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)95,99010
Polymers94,7482
Non-polymers1,2418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)128.516, 128.516, 73.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 77 molecules

#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-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid / Alpha-Ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 14% peg8000, 0.1 M Tris, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2012 / Details: mirrors
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 36801 / Num. obs: 36697 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.056 / Rsym value: 0.048 / Net I/σ(I): 32.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.704 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.64 Å / SU ML: 0.68 / σ(F): 1.33 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 2000 5.46 %
Rwork0.2095 --
obs0.2108 36639 99.71 %
all-36745 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.601 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7165 Å2-0 Å20 Å2
2---0.7165 Å20 Å2
3---1.433 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 38 73 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092580
X-RAY DIFFRACTIONf_angle_d1.0973494
X-RAY DIFFRACTIONf_dihedral_angle_d16.65994
X-RAY DIFFRACTIONf_chiral_restr0.071382
X-RAY DIFFRACTIONf_plane_restr0.005448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0975-2.150.29821400.26292441X-RAY DIFFRACTION100
2.15-2.20810.29041410.24222435X-RAY DIFFRACTION100
2.2081-2.27310.28651400.24332432X-RAY DIFFRACTION100
2.2731-2.34640.28071410.22492440X-RAY DIFFRACTION100
2.3464-2.43030.25941420.2162450X-RAY DIFFRACTION100
2.4303-2.52760.25241410.22312441X-RAY DIFFRACTION100
2.5276-2.64260.29151420.22662473X-RAY DIFFRACTION100
2.6426-2.78190.24081420.2162446X-RAY DIFFRACTION100
2.7819-2.95620.26811430.22762476X-RAY DIFFRACTION100
2.9562-3.18430.2341430.2252464X-RAY DIFFRACTION100
3.1843-3.50460.2691440.20562505X-RAY DIFFRACTION100
3.5046-4.01130.21061440.21042505X-RAY DIFFRACTION100
4.0113-5.05240.18351470.17582539X-RAY DIFFRACTION100
5.0524-40.64790.2361500.21182592X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 3.2422 Å / Origin y: -30.6383 Å / Origin z: 9.4286 Å
111213212223313233
T0.2997 Å20.009 Å2-0.0043 Å2-0.3327 Å20.0631 Å2--0.3294 Å2
L3.3496 °20.5373 °2-0.8275 °2-1.1112 °2-0.246 °2--0.4305 °2
S-0.0746 Å °-0.4064 Å °-0.2127 Å °0.0051 Å °0.0094 Å °0.187 Å °0.05 Å °-0.0097 Å °0.0587 Å °
Refinement TLS groupSelection details: all

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