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- PDB-5fem: Saccharomyces cerevisiae Acetohydroxyacid Synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5fem
TitleSaccharomyces cerevisiae Acetohydroxyacid Synthase in complex with bensulfuron methyl
ComponentsAcetolactate synthase catalytic subunit, mitochondrial
KeywordsTRANSFERASE / Herbicide / sulfonylurea / branched-chain amino acid / acetohydroxyacid synthase / ThDP / FAD / pyruvate
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-60G / FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.168 Å
AuthorsGuddat, L.W. / Lonhienne, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1087713 Australia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Commercial Herbicides Can Trigger the Oxidative Inactivation of Acetohydroxyacid Synthase.
Authors: Lonhienne, T. / Nouwens, A. / Williams, C.M. / Fraser, J.A. / Lee, Y.T. / West, N.P. / Guddat, L.W.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3May 23, 2018Group: Data collection / Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)150,53512
Polymers147,1952
Non-polymers3,34010
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-117 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.673, 154.673, 178.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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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 (strain ATCC 204508 / 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 , 5 types, 567 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-60G / methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate / Bensulfuron methyl


Mass: 410.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N4O7S
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
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
PH range: 6.5

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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 10, 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: 2.168→48.92 Å / Num. obs: 114282 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.129 / Net I/av σ(I): 12.9 / Net I/σ(I): 12.9
Reflection shellResolution: 2.17→2.3 Å / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5233 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0H

1n0h


Resolution: 2.168→48.912 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 2000 1.75 %Random selection
Rwork0.1502 ---
obs0.1506 114267 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.168→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9130 0 218 557 9905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059586
X-RAY DIFFRACTIONf_angle_d0.98413037
X-RAY DIFFRACTIONf_dihedral_angle_d17.343565
X-RAY DIFFRACTIONf_chiral_restr0.061449
X-RAY DIFFRACTIONf_plane_restr0.0041676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1678-2.22210.23531350.19587568X-RAY DIFFRACTION96
2.2221-2.28210.20871410.17137939X-RAY DIFFRACTION100
2.2821-2.34930.1941420.1687951X-RAY DIFFRACTION100
2.3493-2.42510.20641410.16197946X-RAY DIFFRACTION100
2.4251-2.51180.17411430.16227986X-RAY DIFFRACTION100
2.5118-2.61240.19511420.14937957X-RAY DIFFRACTION100
2.6124-2.73120.18231420.14997963X-RAY DIFFRACTION100
2.7312-2.87520.19651420.15388023X-RAY DIFFRACTION100
2.8752-3.05530.19251430.1477976X-RAY DIFFRACTION100
3.0553-3.29120.17771440.13968075X-RAY DIFFRACTION100
3.2912-3.62230.13251420.13068047X-RAY DIFFRACTION100
3.6223-4.14620.15811450.12998120X-RAY DIFFRACTION100
4.1462-5.22290.14151460.13758197X-RAY DIFFRACTION100
5.2229-48.92430.18021520.17838519X-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)
11.0532-0.1577-0.2661.20680.42110.9488-0.00290.0178-0.041-0.02330.0296-0.23750.09390.0977-0.00780.11570.01610.00820.1507-0.00730.2035206.734464.9409236.2998
20.6865-0.8259-0.90161.82161.48961.2391-0.0146-0.19680.06820.20850.1574-0.38460.05830.3437-0.20040.2801-0.0226-0.03870.364-0.04020.382213.815284.7046251.0986
30.85910.37430.02560.96860.03510.42860.0221-0.12710.12570.0598-0.04590.0435-0.075-0.06990.01360.12960.0180.010.185-0.0290.1614186.202588.5897255.1483
40.5426-0.1625-0.00490.8746-0.06390.6060.0039-0.0064-0.0058-0.01050.00130.1492-0.002-0.1667-0.0030.1091-0.01140.00420.2249-0.01160.1811174.548671.2315242.5826
51.0341-0.388-0.26811.76820.25561.20070.03650.21590.0912-0.2208-0.05210.095-0.0776-0.09960.0340.16730.0125-0.02030.24020.01580.1738182.531377.9148218.1594
61.3542-0.8701-0.54162.17380.72451.32650.07010.25290.1636-0.4515-0.0639-0.0556-0.2547-0.0209-0.06090.2809-0.00230.02080.28340.04960.2177188.912585.1066212.3513
71.2785-0.1162-0.21961.71110.38071.77860.1240.20810.0118-0.4407-0.1484-0.23720.05980.2164-0.01190.45010.12140.07240.4619-0.0410.2644203.200454.8493196.8832
80.7888-0.1754-0.42320.7738-0.21361.55220.10640.2154-0.1168-0.4505-0.174-0.08630.25470.15110.02030.41860.07530.01250.366-0.09110.2549198.323449.419201.3533
90.9524-0.28390.11681.07050.0681.00950.04870.0948-0.126-0.0868-0.0463-0.01320.15260.0141-0.00110.2396-0.02490.00680.2601-0.05210.2398189.079251.6451220.9522
101.5841-0.4511-0.37531.42130.25211.41250.01980.0807-0.2901-0.0621-0.07710.2210.278-0.15840.02510.2697-0.0433-0.03720.2349-0.05760.2906180.415442.722223.2399
111.2810.1057-0.36931.8957-0.60213.24120.12860.0605-0.4205-0.093-0.0725-0.05760.34230.10940.06960.42830.0538-0.01190.3928-0.03860.4705205.904536.275223.1255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 255 )
2X-RAY DIFFRACTION2chain 'A' and (resid 256 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 498 )
4X-RAY DIFFRACTION4chain 'A' and (resid 499 through 687 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 205 )
6X-RAY DIFFRACTION6chain 'B' and (resid 206 through 278 )
7X-RAY DIFFRACTION7chain 'B' and (resid 279 through 397 )
8X-RAY DIFFRACTION8chain 'B' and (resid 398 through 498 )
9X-RAY DIFFRACTION9chain 'B' and (resid 499 through 604 )
10X-RAY DIFFRACTION10chain 'B' and (resid 605 through 654 )
11X-RAY DIFFRACTION11chain 'B' and (resid 655 through 687 )

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