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- PDB-1u5b: Crystal structure of the human mitochondrial branched-chain alpha... -

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Basic information

Entry
Database: PDB / ID: 1u5b
TitleCrystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase
Components(2-oxoisovalerate dehydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / KETOACID DEHYDROGENASE / BRANCHED-CHAIN / MULTI-ENZYME COMPLEX / ACYLATION / OXIDATIVE DECARBOXYLATION MAPLE SYRUP URINE DISEASE / THIAMIN DIPHOSPHATE / PHOSPHORYLATION / FLAVOPROTEIN
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 / Branched-chain amino acid catabolism / carboxy-lyase activity / response to nutrient / lipid metabolic process / mitochondrial matrix / 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
: / : / THIAMINE DIPHOSPHATE / 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: 1.83 Å
AuthorsWynn, R.M. / Kato, M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T.
Citation
Journal: Structure / Year: 2004
Title: Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation
Authors: Wynn, R.M. / Kato, M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crosstalk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain A-ketoacid decarboxylase/dehydrogenase
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.M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400SBD MOLECULE DETAILS MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) TRANSFERASE; ...SBD MOLECULE DETAILS MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) TRANSFERASE; FRAGMENT: SUBUNIT-BINDING DOMAIN; EC: 2.3.1.168; GENE: BCATE2; THE SBD MOLECULE WAS CREATED FROM A GENETICALLY MODIFIED SOURCE CONSISTENT WITH THE THE SOURCE RECORDS OF THE ALPHA AND BETA SUBUNITS OF 2-OXOISOVALERATE DEHYDROGENASE FOUND IN THIS STRUCTURE. SEQUENCE: GEIKGRKTLATPAVRRLAMENNIKLSEVVGSGKDGRILKEDILNYLEKQTLEHHHHHH 1 58 RESIDUES 2-50 CORRESPOND TO RESIDUES 165-213 OF SWISSPROT ENTRY ODB2_HUMAN, ACCESSION NUMBER P11182. THE FIRST GLYCINE RESIDUE IS A CLONING ARTIFACT. THE LAST 8 C-TERMINAL RESIDUES (LEHHHHHH) ARE HIS TAG RESIDUES.
Remark 999SEQUENCE The subunit-binding domain (SBD) of the E2 protein binds to the C-terminal region of the ...SEQUENCE The subunit-binding domain (SBD) of the E2 protein binds to the C-terminal region of the E1 beta subunit. However, the electron density of this domain is too weak to build a model, therefore this molecule has not been modeled in the coordinates. Further information on this molecule can be found in Remark 400.

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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)84,1247
Polymers83,4732
Non-polymers6515
Water8,629479
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)168,24814
Polymers166,9474
Non-polymers1,30110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area27690 Å2
ΔGint-168 kcal/mol
Surface area43000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.315, 143.315, 69.294
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-2036-

HOH

DetailsThe biological assembly is a heterotetramer generated from the heterodimer in the asymmetric unit by the operations: x, -y, 2/3-z.

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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: 45571.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCKDHA / Plasmid: PTRCHISB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCKDHB / Plasmid: PTRCHISB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)

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Non-polymers , 5 types, 484 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-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#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.: 479 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG4000, pH 5.8, 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: 1.5418 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9791
ReflectionResolution: 1.83→50 Å / Num. all: 71894 / Num. obs: 71894 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.9
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.889 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
CNS1.1refinement
HKL-2000data collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLS

1ols


Resolution: 1.83→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.868 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19341 1493 2.1 %RANDOM
Rwork0.15604 ---
all0.15684 71866 --
obs0.15604 70373 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.995 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 35 479 6211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.948255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9523.633289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30515995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281543
X-RAY DIFFRACTIONr_chiral_restr0.1320.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024775
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23105
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24285
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2503
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.2227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9841.53718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66426025
X-RAY DIFFRACTIONr_scbond_it2.95732383
X-RAY DIFFRACTIONr_scangle_it4.6274.52230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.831→1.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 104 -
Rwork0.217 5151 -
obs-5225 99.53 %

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