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- PDB-3vad: Crystal structure of I170F mutant branched-chain alpha-ketoacid d... -

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Basic information

Entry
Database: PDB / ID: 3vad
TitleCrystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid
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 / 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
3,6-dichloro-1-benzothiophene-2-carboxylic acid / ADENOSINE-5'-DIPHOSPHATE / : / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsAhmed, K. / Gui, W.J. / Tso, S.C. / Chuang, J.L. / Wynn, R.M. / Chuang, D.T.
CitationJournal: To be Published
Title: Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid
Authors: Ahmed, K. / Gui, W.J. / Tso, S.C. / Chuang, J.L. / M Wynn, R. / Chuang, D.T.
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
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

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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)48,3936
Polymers47,4081
Non-polymers9855
Water362
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)96,78612
Polymers94,8172
Non-polymers1,97010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area10680 Å2
ΔGint-83 kcal/mol
Surface area56390 Å2
Unit cell
Length a, b, c (Å)128.079, 128.079, 74.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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: 47408.262 Da / Num. of mol.: 1 / Mutation: F170I
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): BL21-GroESL
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase

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Non-polymers , 5 types, 7 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-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-0F1 / 3,6-dichloro-1-benzothiophene-2-carboxylic acid


Mass: 247.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H4Cl2O2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG8000, 0.1 M Tris, 1.9 M NaCl, 250mM KCl, 400mM Arg-HCl,2mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2011
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 19456 / Num. obs: 19442 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.074 / Rsym value: 0.087 / Net I/σ(I): 24
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.31 / Num. unique all: 958 / Rsym value: 0.746 / % possible all: 100

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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: 2.602→40.502 Å / SU ML: 0.81 / σ(F): 0.13 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 991 5.13 %random
Rwork0.2264 ---
obs0.2288 19328 99.35 %-
all-19454 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.652 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.261 Å2-0 Å20 Å2
2---0.261 Å20 Å2
3---0.522 Å2
Refinement stepCycle: LAST / Resolution: 2.602→40.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 57 2 2564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112674
X-RAY DIFFRACTIONf_angle_d1.373632
X-RAY DIFFRACTIONf_dihedral_angle_d16.1831009
X-RAY DIFFRACTIONf_chiral_restr0.085394
X-RAY DIFFRACTIONf_plane_restr0.005462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6015-2.73870.36051410.28522529X-RAY DIFFRACTION98
2.7387-2.91020.36721540.2722536X-RAY DIFFRACTION100
2.9102-3.13480.28481330.25132589X-RAY DIFFRACTION99
3.1348-3.45020.30961530.24192592X-RAY DIFFRACTION99
3.4502-3.9490.25811480.22592603X-RAY DIFFRACTION100
3.949-4.97390.24591410.19962661X-RAY DIFFRACTION100
4.9739-40.5070.26161210.22092827X-RAY DIFFRACTION100

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