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- PDB-6bd3: Saccharomyces cerevisiae acetohydroxyacid synthase -

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Basic information

Entry
Database: PDB / ID: 6bd3
TitleSaccharomyces cerevisiae acetohydroxyacid synthase
ComponentsAcetolactate synthase catalytic subunit, mitochondrial
KeywordsTRANSFERASE / AHAS / FAD / 2-hydroxyethyl-ThDP / dioxygen
Function / homology
Function and homology information


acetolactate synthase complex / acetolactate synthase activity / acetolactate synthase / branched-chain amino acid biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion
Similarity search - Function
Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding ...Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CARBON DIOXIDE / FLAVIN-ADENINE DINUCLEOTIDE / 2-ACETYL-THIAMINE DIPHOSPHATE / : / OXYGEN MOLECULE / PHOSPHATE ION / THIAMINE DIPHOSPHATE / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.28 Å
AuthorsGuddat, L.W. / Lonhienne, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1087713 Australia
CitationJournal: Chemistryselect / Year: 2017
Title: High resolution crystal structures of the acetohydroxyacid synthase-pyruvate complex provide new insights into its catalytic mechanism
Authors: Lonhienne, T. / Garcia, M.D. / Noble, C. / Harmer, J. / Fraser, J.A. / Williams, C.M. / Guddat, L.W.
History
DepositionOct 21, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionNov 8, 2017ID: 5INV
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase catalytic subunit, mitochondrial
B: Acetolactate synthase catalytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,24021
Polymers147,1952
Non-polymers3,04519
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-75 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.898, 108.766, 180.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetolactate synthase catalytic subunit, mitochondrial / Acetohydroxy-acid synthase catalytic subunit / ALS


Mass: 73597.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ILV2, SMR1, YMR108W, YM9718.07 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P07342, acetolactate synthase

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Non-polymers , 10 types, 339 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-HTL / 2-ACETYL-THIAMINE DIPHOSPHATE / 2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZO LIUM INNER SALT P,P'-DIOXIDE


Mass: 467.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N4O8P2S
#9: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#10: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 34 mg/ml enzyme incubated with 1.4 mM ThDP, 0.5 mM FAD, 14 mM MgCl2, 0.7 mM BSM and 4.5 mM DTT. Crystals were obtained my mixing equal volumes (300 nl) of well solution (1.6M Na/K hydrogen ...Details: 34 mg/ml enzyme incubated with 1.4 mM ThDP, 0.5 mM FAD, 14 mM MgCl2, 0.7 mM BSM and 4.5 mM DTT. Crystals were obtained my mixing equal volumes (300 nl) of well solution (1.6M Na/K hydrogen phosphate pH 6.5) and complex solution. Crystals were soaked with pyruvate (pyruvate powder added to the drop) for three weeks
PH range: 5.7-5.9

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford cryostream
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2014 / Details: Mirrors
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.28→47.94 Å / Num. obs: 86039 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.077 / Net I/av σ(I): 11.8 / Net I/σ(I): 11.8
Reflection shellResolution: 2.28→2.31 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.8 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.28→47.306 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1999 2.32 %
Rwork0.171 --
obs0.1718 86040 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→47.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8310 0 193 320 8823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048665
X-RAY DIFFRACTIONf_angle_d0.84211769
X-RAY DIFFRACTIONf_dihedral_angle_d15.1213169
X-RAY DIFFRACTIONf_chiral_restr0.0541331
X-RAY DIFFRACTIONf_plane_restr0.0031508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2805-2.33750.31481340.25165677X-RAY DIFFRACTION95
2.3375-2.40070.21431410.23395931X-RAY DIFFRACTION100
2.4007-2.47130.24721420.23315949X-RAY DIFFRACTION100
2.4713-2.55110.2821410.21435944X-RAY DIFFRACTION100
2.5511-2.64230.25131420.20365974X-RAY DIFFRACTION100
2.6423-2.7480.23551430.20215981X-RAY DIFFRACTION100
2.748-2.87310.23891420.19546000X-RAY DIFFRACTION100
2.8731-3.02450.221430.18715996X-RAY DIFFRACTION100
3.0245-3.2140.20611430.17726008X-RAY DIFFRACTION100
3.214-3.46210.21241440.15726023X-RAY DIFFRACTION100
3.4621-3.81030.16681430.15156041X-RAY DIFFRACTION100
3.8103-4.36140.16051440.13626075X-RAY DIFFRACTION100
4.3614-5.49360.17391470.14126118X-RAY DIFFRACTION100
5.4936-47.31590.18571500.17486324X-RAY DIFFRACTION99
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)
10.95410.6305-0.58051.2514-0.59010.94880.1162-0.16550.03310.1651-0.182-0.0815-0.09280.3680.07520.2369-0.05790.00220.38010.010.1982212.8107126.59205.1256
20.5254-0.33380.14531.0239-1.44643.01010.0415-0.0353-0.2446-0.16540.04620.1740.3771-0.1679-0.08310.3361-0.07090.00480.2781-0.00870.3069195.0215102.629205.3618
33.0108-0.4927-1.80141.6393-0.41663.26060.06340.1323-0.00770.0746-0.15620.43380.0541-0.63440.11640.218-0.07550.00590.5005-0.07810.3315175.1052133.4131200.5843
41.8734-0.0489-0.66342.23240.39262.70740.1381-0.20830.42840.1853-0.05480.121-0.5236-0.1799-0.04660.2961-0.00160.03520.3014-0.08950.3325183.7855145.2442206.2879
50.69620.6342-1.15593.35320.7023.10320.52560.07870.9709-0.53570.2471-0.5853-2.27870.7239-0.62031.3244-0.21980.30510.6823-0.00341.0039195.3514164.9696189.0559
60.290.40390.22094.73510.3511.41110.2230.42220.2566-0.629-0.1937-0.6922-0.470.5836-0.1660.4106-0.0410.1010.70540.16470.4224196.7134148.5438170.7526
71.3490.2311-0.11123.5221-0.10272.90330.05830.30820.1194-0.1425-0.0618-0.3340.00030.279-0.02810.19950.0231-0.00960.44060.03950.2267194.7133135.3633179.8302
87.3594-1.2711-3.7668.4808-1.30924.42750.18030.4440.1017-0.3191-0.1865-0.50360.01360.0449-0.07860.2719-0.0055-0.0260.53920.06260.2234192.2677134.5798167.802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 648 )
3X-RAY DIFFRACTION3chain 'B' and (resid 84 through 163 )
4X-RAY DIFFRACTION4chain 'B' and (resid 164 through 315 )
5X-RAY DIFFRACTION5chain 'B' and (resid 316 through 450 )
6X-RAY DIFFRACTION6chain 'B' and (resid 451 through 498 )
7X-RAY DIFFRACTION7chain 'B' and (resid 499 through 621 )
8X-RAY DIFFRACTION8chain 'B' and (resid 622 through 649 )

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