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- PDB-1v11: CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP C... -

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Basic information

Entry
Database: PDB / ID: 1v11
TitleCROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE
Components(2-OXOISOVALERATE DEHYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / KETOACID DEHYDROGENASE / BRANCHED-CHAIN / MULTI-ENZYME COMPLEX / ACYLATION / OXIDATIVE DECARBOXYLATION / MAPLE SYRUP URINE DISEASE / THIAMINE PHOSPHATE / PHOSPHORYLATION
Function / homology
Function and homology information


3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / : / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / Glyoxylate metabolism and glycine degradation / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient ...3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / : / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / Glyoxylate metabolism and glycine degradation / 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
Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / 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 ...Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / 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
BENZAMIDINE / : / : / 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: 1.95 Å
AuthorsLi, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Cross-Talk between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-Chain {Alpha}-Keto Acid Decarboxylase/Dehydrogenase
Authors: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 2003
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.
#3: Journal: Structure / Year: 2000
Title: Crystal Structure of Human Branched-Chain Alpha-Ketoacid Dehydrogenase and the Molecular Basis of Multienzyme Complex Deficiency in Maple Syrup Urine Disease
Authors: Aevarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G.J.
History
DepositionApr 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
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 2.1Dec 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)84,45215
Polymers83,3202
Non-polymers1,13213
Water9,530529
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)168,90530
Polymers166,6404
Non-polymers2,26426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area30620 Å2
ΔGint-243.2 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.505, 145.505, 69.172
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
11A-2185-

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 / MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT ALPHA CHAIN / ...MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT ALPHA CHAIN / BCKDH E1-ALPHA / BCKDE1A


Mass: 45417.914 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: EXPRESSION SYSTEM USED BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES
Plasmid: PTRC-ALPHA-BETAHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21
References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#2: Protein 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT / MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT BETA CHAIN / ...MITOCHONDRIAL PRECURSOR / 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)
Description: EXPRESSION SYSTEM USED BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES
Plasmid: PTRC-ALPHA-BETAHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21
References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)

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Non-polymers , 7 types, 542 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION IN CHAIN A, ARG 332 TO ALA FUNCTION: THE BRANCHED-CHAIN ALPHA-KETO ...ENGINEERED MUTATION IN CHAIN A, ARG 332 TO ALA FUNCTION: THE BRANCHED-CHAIN ALPHA-KETO DEHYDROGENASE COMPLEX CATALYZES THE OVERALL CONVERSION OF ALPHA-KETO ACIDS TO ACYL-COA AND CO(2).

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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: 293 K / Method: vapor diffusion / pH: 5.5
Details: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) ...Details: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) GLYCEROL) WITH WELL SOLUTION (1.4-1.6 M AMMONIUM SULFATE, 0.1 M NA-CITRATE PH 5.8, 20 MM B-MERCAPTOETHANOL). SERIALLY DILUTED CRUSHED CRYSTALS WERE USED FOR MICRO-SEEDING ONE DAY AFTER THE DROPS WERE SET UP. CRYSTALS APPEARED ONE DAY AFTER SEEDING AND GREW TO A MAXIMUM SIZE OF 120 X 800 UM WITHIN 10 DAYS. CRYSTALS WERE STABILIZED FOR 12 HOURS BY TRANSFER TO FRESH WELL SOLUTION. THEY WERE THEN CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER CONTAINING 1.6 M AMMONIUM SULFATE, 50 MM HEPES, PH 7.5, 100 MM NA-CITRATE, PH 5.8, 100 MM KCL, 50 MM DTT AND UP TO 20% (V/V) GLYCEROL. IT WAS FOUND THAT MN2+ IONS COULD REPLACE THE MG2+ REQUIRED FOR THE BINDING OF THDP TO THE ENZYME.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00691
DetectorDetector: CCD / Date: Jul 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00691 Å / Relative weight: 1
ReflectionResolution: 1.95→33.35 Å / Num. obs: 61649 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OLS

1ols


Resolution: 1.95→27.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.456 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1486 2.4 %RANDOM
Rwork0.138 ---
obs0.139 60094 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 61 529 6171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215849
X-RAY DIFFRACTIONr_bond_other_d0.0040.025178
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9527940
X-RAY DIFFRACTIONr_angle_other_deg1.46312061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026597
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021234
X-RAY DIFFRACTIONr_nbd_refined0.2150.21243
X-RAY DIFFRACTIONr_nbd_other0.2710.25939
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.23065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2398
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.2258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.53575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83525773
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.97232274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8084.52167
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 96
Rwork0.184 4408
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)
10.80930.1625-1.0175-0.1301-0.41050.16090.0399-0.06470.0255-0.00170.11630.4589-0.2505-0.1692-0.15610.0798-0.00890.0150.07830.04560.096348.694-6.38431.845
20.3105-0.01140.06350.1587-0.12490.3280.00720.0434-0.001-0.01340.03430.0314-0.051-0.0354-0.04150.08490.015-0.00470.0456-0.00080.077565.29416.2055.627
30.4585-0.4369-0.09790.42790.02270.1393-0.00730.03390.1208-0.0241-0.0521-0.0868-0.11850.110.05940.0553-0.0610.0210.09420.02140.0817101.59618.6667.151
4-10.9602-13.2237-4.609130.5142-2.67274.00970.21850.37710.37060.88070.3377-0.1377-0.05610.4096-0.55620.08260-0.00050.082400.0823100.4043.07350.49
50.1172-0.0260.04240.1277-0.10730.34930.0091-0.01430.01730.0365-0.0131-0.0066-0.0680.04830.0040.0958-0.0178-0.00450.0501-0.02830.0884.47512.38234.958
60.2362-0.06-0.0260.3798-0.02550.38230.0101-0.0399-0.00340.0656-0.0284-0.0871-0.02670.15020.01830.0314-0.0267-0.03890.1157-0.00510.078106.9053.73537.526
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

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