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- PDB-5wkc: Saccharomyces cerevisiae acetohydroxyacid synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5wkc
TitleSaccharomyces cerevisiae acetohydroxyacid synthase in complex with the herbicide penoxsulam
Components(Acetolactate synthase catalytic subunit, ...) x 2
KeywordsSTRUCTURAL PROTEIN / Transferase / AHAS / acetohydroxyacid synthase / ScAHAS / thiamine diphosphate / flavin adenine dinucleotide / penoxsulam / aminoethenethiol diphosphate / peracetate.
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
Chem-AUJ / ETHANEPEROXOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Chem-PXD / Chem-TP9 / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.334 Å
AuthorsGuddat, W.L. / Lonhienne, G.T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1008736 Australia
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural insights into the mechanism of inhibition of AHAS by herbicides.
Authors: Lonhienne, T. / Garcia, M.D. / Pierens, G. / Mobli, M. / Nouwens, A. / Guddat, L.W.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 25, 2022Group: Database references / Derived calculations / Non-polymer description
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Acetolactate synthase catalytic subunit, mitochondrial
D: Acetolactate synthase catalytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,54623
Polymers294,4074
Non-polymers7,13919
Water21,1141172
1
A: Acetolactate synthase catalytic subunit, mitochondrial
D: Acetolactate synthase catalytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,78711
Polymers147,2112
Non-polymers3,5769
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-82 kcal/mol
Surface area39530 Å2
MethodPISA
2
B: Acetolactate synthase catalytic subunit, mitochondrial
E: Acetolactate synthase catalytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,75812
Polymers147,1952
Non-polymers3,56310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-104 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.213, 218.213, 361.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Acetolactate synthase catalytic subunit, ... , 2 types, 4 molecules ABED

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


Mass: 73597.656 Da / Num. of mol.: 3 / Fragment: UNP residues 58-687
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ILV2, SMR1, YMR108W, YM9718.07 / Production host: Escherichia coli (E. coli) / References: UniProt: P07342, acetolactate synthase
#2: Protein Acetolactate synthase catalytic subunit, mitochondrial / Acetohydroxy-acid synthase catalytic subunit / ALS


Mass: 73613.664 Da / Num. of mol.: 1 / Fragment: UNP residues 58-687
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ILV2, SMR1, YMR108W, YM9718.07 / Production host: Escherichia coli (E. coli) / References: UniProt: P07342, acetolactate synthase

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Non-polymers , 7 types, 1191 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PXD / 2-(2,2-difluoroethoxy)-N-(5,8-dimethoxy[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)-6-(trifluoromethyl)benzenesulfonamide / Penoxsulam


Mass: 483.370 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14F5N5O5S
#5: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-F50 / ETHANEPEROXOIC ACID


Mass: 76.051 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O3
#7: Chemical ChemComp-AUJ / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(1~{S})-1-(dioxidanyl)-1-oxidanyl-ethyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 501.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N4O10P2S
#8: Chemical ChemComp-TP9 / (3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE


Mass: 412.296 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N4O7P2S
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1172 / 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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 M succinic acid pH 7.0, 0.1 M HEPES pH 7.0 and 1% w/v polyethylene glycol monomethyl ether 2,000.
PH range: 6.8 - 7.2

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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: Feb 16, 2013 / 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: 2.33→48.79 Å / Num. obs: 183012 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Net I/σ(I): 11.1
Reflection shellResolution: 2.33→2.37 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.751 / Num. unique obs: 8829 / Rpim(I) all: 0.316 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0H

1n0h


Resolution: 2.334→48.794 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 2000 1.09 %
Rwork0.1504 --
obs0.1507 182982 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.334→48.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18144 0 465 1172 19781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819091
X-RAY DIFFRACTIONf_angle_d0.91725972
X-RAY DIFFRACTIONf_dihedral_angle_d14.2647131
X-RAY DIFFRACTIONf_chiral_restr0.0372882
X-RAY DIFFRACTIONf_plane_restr0.0033337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3338-2.39210.24951390.212412638X-RAY DIFFRACTION99
2.3921-2.45680.22531420.206112807X-RAY DIFFRACTION100
2.4568-2.52910.22821420.189712855X-RAY DIFFRACTION100
2.5291-2.61070.22461410.179612789X-RAY DIFFRACTION100
2.6107-2.7040.19031420.174612880X-RAY DIFFRACTION100
2.704-2.81230.22341430.181112840X-RAY DIFFRACTION100
2.8123-2.94020.22241420.172612889X-RAY DIFFRACTION100
2.9402-3.09520.20021420.163312860X-RAY DIFFRACTION100
3.0952-3.28910.17591430.157512902X-RAY DIFFRACTION100
3.2891-3.5430.18991420.144712949X-RAY DIFFRACTION100
3.543-3.89940.16011440.132512983X-RAY DIFFRACTION100
3.8994-4.46330.1541440.120313006X-RAY DIFFRACTION100
4.4633-5.6220.14911450.121713110X-RAY DIFFRACTION100
5.622-48.80460.14141490.136813474X-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)
12.05640.03050.21561.61130.04261.1709-0.00020.37760.0512-0.26080.0107-0.2105-0.05640.2303-0.00810.2081-0.04020.05110.25230.00190.188228.9248474.00440.2435
28.6571.0526.66980.17770.86845.16040.40241.4407-0.5325-0.29590.0414-0.21590.47950.8944-0.42160.60870.0180.0020.8454-0.05150.317121.5023465.36418.0725
30.9109-0.0051-0.07210.77960.13580.8421-0.00580.34610.1677-0.2267-0.00660.1041-0.1403-0.16360.02030.31130.0036-0.05610.32890.09530.2515-1.7871483.301234.0487
40.5595-0.23110.16320.979-0.56090.78440.0084-0.0021-0.1187-0.0260.01280.13170.0873-0.0317-0.03150.1649-0.0308-0.01670.1744-0.01860.274319.9853458.0303115.3545
50.68310.06750.0870.40070.04310.6259-0.0125-0.00720.1563-0.01070.0048-0.0015-0.16130.07580.01080.2173-0.0545-0.02730.1824-0.01540.283829.3442480.6568111.2466
61.8016-0.35130.16062.4658-0.28621.2891-0.0076-0.36870.16540.47950.00810.0858-0.1663-0.01190.0030.2973-0.06140.01090.2998-0.0760.216825.8836476.568141.4778
71.3384-3.29463.18659.5174-9.49759.4071-0.3021-0.9877-0.08361.04590.88290.7552-0.2902-1.2035-0.65470.9054-0.01260.12860.98890.05160.57820.4427466.6842163.8899
81.0803-0.0626-0.35271.3317-0.02541.0894-0.0406-0.6268-0.28650.63040.0355-0.04960.2180.19640.00370.5901-0.0027-0.12720.62260.13630.37741.2921449.9186156.2126
91.10850.18420.08931.9732-0.03530.75830.0006-0.1868-0.1980.22920.0074-0.33240.10220.2555-0.02050.2674-0.0134-0.10940.3760.03970.359250.7239451.7185133.9492
101.7635-0.00460.11841.1440.03351.2363-0.01680.0242-0.1229-0.02180.00990.08990.0398-0.0990.01560.1337-0.0204-0.0040.121-0.00540.17044.7305464.755759.2184
112.9281-0.34510.86620.31080.18220.52330.1242-0.3978-0.50250.1595-0.07590.10490.1348-0.2625-0.05710.2178-0.0597-0.02280.22140.03360.30330.8355455.480860.1831
121.72980.2565-0.07041.9191-0.11952.16070.0244-0.0585-0.07340.2154-0.0569-0.20920.1350.23980.02080.17610.0084-0.05560.1691-0.00620.229236.4494459.814679.0773
131.39120.1125-0.02980.54180.11160.75070.0184-0.05960.20360.019-0.0034-0.123-0.180.1609-0.01760.2158-0.0575-0.01540.1528-0.00360.263229.0411486.847667.4534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 255 )
2X-RAY DIFFRACTION2chain 'A' and (resid 256 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 687 )
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 366 )
5X-RAY DIFFRACTION5chain 'B' and (resid 367 through 687 )
6X-RAY DIFFRACTION6chain 'E' and (resid 84 through 255 )
7X-RAY DIFFRACTION7chain 'E' and (resid 256 through 298 )
8X-RAY DIFFRACTION8chain 'E' and (resid 299 through 542 )
9X-RAY DIFFRACTION9chain 'E' and (resid 543 through 687 )
10X-RAY DIFFRACTION10chain 'D' and (resid 84 through 238 )
11X-RAY DIFFRACTION11chain 'D' and (resid 239 through 278 )
12X-RAY DIFFRACTION12chain 'D' and (resid 279 through 457 )
13X-RAY DIFFRACTION13chain 'D' and (resid 458 through 687 )

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