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- PDB-6bd9: Saccharomyces cerevisiae acetohydroxyacid synthase -

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Basic information

Entry
Database: PDB / ID: 6bd9
TitleSaccharomyces cerevisiae acetohydroxyacid synthase
ComponentsAcetolactate synthase catalytic subunit, mitochondrial
KeywordsTRANSFERASE / AHAS / pyruvate / FAD / dioxygen
Function / homology
Function and homology information


acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / L-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
FLAVIN-ADENINE DINUCLEOTIDE / : / OXYGEN MOLECULE / PHOSPHATE ION / PYRUVIC ACID / THIAMINE DIPHOSPHATE / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.982 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 22, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionNov 8, 2017ID: 5INU
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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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)150,44723
Polymers147,1952
Non-polymers3,25221
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12510 Å2
ΔGint-56 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.024, 110.967, 180.244
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) / References: UniProt: P07342, acetolactate synthase

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Non-polymers , 8 types, 656 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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#7: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
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 then soaked with pyruvate (added as powder in the drop) for 2 hours
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: Mar 28, 2015 / 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: 1.98→50 Å / Num. obs: 127729 / % possible obs: 95.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.104 / Net I/av σ(I): 29.8 / Net I/σ(I): 29.8
Reflection shellResolution: 1.982→2.169 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 2.6 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.982→29.929 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1813 1999 1.57 %
Rwork0.1589 --
obs0.1592 127477 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.982→29.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8398 0 207 635 9240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0198814
X-RAY DIFFRACTIONf_angle_d1.74511976
X-RAY DIFFRACTIONf_dihedral_angle_d17.5783251
X-RAY DIFFRACTIONf_chiral_restr0.1031347
X-RAY DIFFRACTIONf_plane_restr0.0091543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9817-2.03120.24621310.23928274X-RAY DIFFRACTION90
2.0312-2.08610.25091350.2288425X-RAY DIFFRACTION90
2.0861-2.14750.27251350.2098439X-RAY DIFFRACTION91
2.1475-2.21680.20121350.18748479X-RAY DIFFRACTION91
2.2168-2.2960.20021350.17958493X-RAY DIFFRACTION91
2.296-2.38790.20071370.17598638X-RAY DIFFRACTION93
2.3879-2.49650.21231430.17628885X-RAY DIFFRACTION95
2.4965-2.62810.16891440.16299060X-RAY DIFFRACTION97
2.6281-2.79260.17731460.16949211X-RAY DIFFRACTION98
2.7926-3.0080.1991500.17499364X-RAY DIFFRACTION99
3.008-3.31040.21811490.1639396X-RAY DIFFRACTION100
3.3104-3.78860.17761510.14359456X-RAY DIFFRACTION100
3.7886-4.77010.13771530.12329532X-RAY DIFFRACTION100
4.7701-29.93260.15041550.14369826X-RAY DIFFRACTION100
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)
11.38550.7032-0.54480.98920.051.43770.0855-0.14770.05360.1104-0.107-0.0955-0.03240.31080.01490.1447-0.0265-0.01330.20930.02680.1542213.592131.406423.0631
20.3917-0.28860.16221.0323-1.34842.45160.0227-0.0504-0.1731-0.11020.05330.15470.2721-0.1398-0.0490.2283-0.045-0.00290.1624-0.00060.2279195.7934105.546927.0341
31.60060.2034-0.39051.12540.29211.95750.0328-0.04320.03430.0644-0.07720.22560.0065-0.34440.0330.1352-0.02290.01740.2082-0.03520.1901180.6049137.743125.1943
40.4293-0.663-0.54870.64370.75412.27020.4172-0.07160.59110.055-0.1224-0.2062-1.5291-0.1976-0.15880.93740.03580.12220.3639-0.04290.6935181.7675163.760122.7023
50.6273-0.0673-0.0932.67940.75992.81830.51150.00510.7845-0.89020.3298-0.4557-2.49151.0928-0.34191.372-0.30990.34210.52030.0280.8045197.2477165.92295.5408
61.0533-0.18520.37951.7051-0.43892.41870.05020.31310.1706-0.1458-0.1027-0.2091-0.07670.28040.00080.1456-0.0040.01170.27250.05040.1832194.2711139.4549-2.9714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 271 )
2X-RAY DIFFRACTION2chain 'A' and (resid 280 through 648 )
3X-RAY DIFFRACTION3chain 'B' and (resid 83 through 255 )
4X-RAY DIFFRACTION4chain 'B' and (resid 256 through 315 )
5X-RAY DIFFRACTION5chain 'B' and (resid 316 through 472 )
6X-RAY DIFFRACTION6chain 'B' and (resid 473 through 646 )

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