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- PDB-2bfc: Reactivity modulation of human branched-chain alpha-ketoacid dehy... -

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Basic information

Entry
Database: PDB / ID: 2bfc
TitleReactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch
Components(2-OXOISOVALERATE DEHYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / OXIDATIVE DECARBOXYLATION / MAPLE SYRUP URINE DISEASE / THIAMINE DIPHOSPHATE / PHOSPHORYLATION / CONFORMATIONAL SWITCH
Function / homology
Function and homology information


Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process ...Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process / oxoglutarate dehydrogenase complex / Branched-chain amino acid catabolism / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient / lipid metabolic process / mitochondrial matrix / protein-containing complex binding / nucleolus / mitochondrion / nucleoplasm / metal ion binding
Similarity search - Function
: / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II ...: / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / Chem-TZD / 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial / 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMachius, M. / Wynn, R.M. / Chuang, J.L. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T.
Citation
Journal: Structure / Year: 2006
Title: A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase.
Authors: Machius, M. / Wynn, R.M. / Chuang, J.L. / Li, J. / Kluger, R. / Yu, D. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crosstalk between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine
Authors: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Roles of His291-Alpha and His146-Beta in the Reductive Acylation Reaction Catalyzed by Human Branched-Chain Alpha-Ketoacid Dehydrogenase: Refined Phosphorylation Loop Structure in the Active Site
Authors: Wynn, R. / Machius, M. / Chuang, J. / Li, J. / Tomchick, D. / Chuang, D.
#3: Journal: J.Biol.Chem. / Year: 2001
Title: Roles of Active Site and Novel K+ Ion-Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase/Dehydrogenase
Authors: Wynn, R.M. / Ho, R. / Chuang, J.L. / Chuang, D.T.
History
DepositionDec 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _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: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0407
Polymers83,3742
Non-polymers6665
Water11,061614
1
A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
hetero molecules

A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,08014
Polymers166,7494
Non-polymers1,33110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area27530 Å2
ΔGint-157.7 kcal/mol
Surface area43280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.341, 145.341, 69.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2105-

HOH

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Components

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2-OXOISOVALERATE DEHYDROGENASE ... , 2 types, 2 molecules AB

#1: Protein 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN / BCKDH E1-ALPHA / BCKDE1A


Mass: 45472.031 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-445 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRC-ALPHA-BETAHIS / Production host: ESCHERICHIA COLI (E. coli)
Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES
References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#2: Protein 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN / BCKDH E1-BETA


Mass: 37902.270 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRC-ALPHA-BETAHIS / Production host: ESCHERICHIA COLI (E. coli)
Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES
References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)

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Non-polymers , 5 types, 619 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 113 FROM TYR 3-METHYL-2-OXOBUTANOATE + [DIHYDROLIPOYLLYSINE- ...ENGINEERED RESIDUE IN CHAIN A, PHE 113 FROM TYR 3-METHYL-2-OXOBUTANOATE + [DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL)TRANSFERASE] LIPOYLLYSINE ==> [DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) TRANSFERASE] S-(2-METHYLPROPANOYL)DIHYDROLIPOYLLYSINE + CO2

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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: 2.5 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: CRYSTALS WERE GROWN AT 22C VIA THE VAPOR DIFFUSION METHOD IN COMPLEX WITH A 40 AMINO ACID PEPTIDE DERIVED FROM THE SUBUNIT BINDING DOMAIN (SBD) OF THE E2 COMPONENT OF BRANCHED CHAIN ALPHA- ...Details: CRYSTALS WERE GROWN AT 22C VIA THE VAPOR DIFFUSION METHOD IN COMPLEX WITH A 40 AMINO ACID PEPTIDE DERIVED FROM THE SUBUNIT BINDING DOMAIN (SBD) OF THE E2 COMPONENT OF BRANCHED CHAIN ALPHA-KETOACID DEHDROGENASE. THIS COMPLEX WAS FORMED BY MIXING N-TERMINALLY HIS6-TAGGED PROTEIN WITH C-TERMINALLY HIS6-TAGGED SBD IN 50 MM NA-HEPES, PH 7.5, 150 MM KCL, 20 MM DTT AND 5% (V/V) GLYCEROL AT A MOLAR RATIO OF 1:4. CRYSTALS OF THE COMPLEX (20 MG/ML) WERE OBTAINED BY MIXING 3 MICROLITERS OF PROTEIN WITH 3 MICROLITERS OF CRYSTALLIZATION SOLUTION (10% (V/V) POLYETHYLENE GLYCOL 4000, 10% (V/V) MPD AND 0.1M SODIUM CITRATE, PH 5.8) WITH 1 ML OF CRYSTALLIZATION SOLUTION IN THE RESERVOIR. MANGANESE IONS WERE USED INSTEAD OF MAGNESIUM REQUIRED FOR THE BINDING OF THIAMIN DIPHOSPHATE TO THE ENZYME. THE PRESENCE OF MANGANESE IONS IN THE CRYSTALS RESULTED IN IMPROVED X-RAY DIFFRACTION QUALITIES WITHOUT AFFECTING THE CATALYTIC PROPERTIES. CRYSTALS WERE CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER (CRYSTALLIZATION SOLUTION CONTAINING 5-10%(V/V) GLYCEROL).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00691
DetectorType: CUSTOM / Detector: CCD / Date: Aug 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00691 Å / Relative weight: 1
ReflectionResolution: 1.64→35.88 Å / Num. obs: 100584 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 16.08 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.9
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OLS

1ols


Resolution: 1.64→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.411 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 1493 1.5 %RANDOM
Rwork0.144 ---
obs0.144 99084 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 36 614 6210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.921.9428316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5923.507288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.493151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4351545
X-RAY DIFFRACTIONr_chiral_restr0.1450.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024829
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.23109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.24361
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2188
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.257
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0951.53738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82826082
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.02432391
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6714.52234
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 99
Rwork0.163 6758
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53590.2172-0.93850.1857-0.2022.29350.0381-0.0380.11930.07020.09280.3969-0.1272-0.0968-0.13090.0108-0.00120.03270.0220.03210.093848.658-6.19331.963
20.5196-0.01990.02340.4219-0.1780.68510.01410.10580.0432-0.06370.0190.0634-0.1194-0.0558-0.03310.0190.0175-0.0094-0.04070.0066-0.024365.13516.4665.835
30.7013-0.36670.02731.0205-0.0480.0024-0.0010.16010.1581-0.1477-0.0897-0.1793-0.14790.31260.09070.0028-0.07830.0350.10580.0476-0.0004101.69318.5856.779
456.318951.45665.439849.47962.418278.8403-0.1222-1.4599-0.77663.1161-0.3703-0.784-0.5967-0.20660.4925-0.00880.0027-0.002-0.0067-0.0058-0.007699.012-1.09149.31
50.27360.07350.00470.3656-0.09850.66030.0316-0.04610.05180.0964-0.0323-0.0254-0.14640.12670.00070.0159-0.0374-0.0075-0.0294-0.013-0.031884.58812.48734.836
60.53540.0731-0.12130.6853-0.1010.75860.0198-0.099-0.01170.1205-0.0585-0.2313-0.05490.32320.0388-0.0732-0.0399-0.05460.0960.0153-0.0166107.0223.79337.437
712.8379-2.24085.17330.399-0.73625.605-0.050.23660.1034-0.13060.04860.0961-0.16850.01970.00140.08580.00440.01280.0066-0.00930.06373.3692.7657.907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 30
2X-RAY DIFFRACTION2A31 - 355
3X-RAY DIFFRACTION3A356 - 400
4X-RAY DIFFRACTION4B1002 - 1007
5X-RAY DIFFRACTION5B1014 - 1191
6X-RAY DIFFRACTION6B1192 - 1342
7X-RAY DIFFRACTION7A601

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