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- PDB-1t9a: Crystal structure of yeast acetohydroxyacid synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 1t9a
TitleCrystal structure of yeast acetohydroxyacid synthase in complex with a sulfonylurea herbicide, tribenuron methyl
ComponentsAcetolactate synthase, mitochondrial
KeywordsTRANSFERASE / acetohydroxyacid synthase / acetolactate synthase / herbicide / sulfonylurea / thiamin diphosphate / FAD / inhibitor / tribenuron methyl
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-1TB / FLAVIN-ADENINE DINUCLEOTIDE / : / PROPYL TRIHYDROGEN DIPHOSPHATE / Chem-YF3 / Chem-YF4 / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMcCourt, J.A. / Pang, S.S. / Guddat, L.W. / Duggleby, R.G.
CitationJournal: Biochemistry / Year: 2005
Title: Elucidating the specificity of binding of sulfonylurea herbicides to acetohydroxyacid synthase.
Authors: McCourt, J.A. / Pang, S.S. / Guddat, L.W. / Duggleby, R.G.
History
DepositionMay 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / struct_ref_seq_dif / struct_site
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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)150,51714
Polymers147,1952
Non-polymers3,32112
Water16,448913
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-64 kcal/mol
Surface area38560 Å2
MethodPISA
2
A: Acetolactate synthase, mitochondrial
B: Acetolactate synthase, mitochondrial
hetero molecules

A: Acetolactate synthase, mitochondrial
B: Acetolactate synthase, mitochondrial
hetero molecules

A: Acetolactate synthase, mitochondrial
B: Acetolactate synthase, mitochondrial
hetero molecules

A: Acetolactate synthase, mitochondrial
B: Acetolactate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)602,06756
Polymers588,7818
Non-polymers13,28548
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area64020 Å2
ΔGint-288 kcal/mol
Surface area144580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.586, 154.586, 178.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsThe asymmetric unit contains the minimum biological unit required for activity, a dimer.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 73597.656 Da / Num. of mol.: 2 / Fragment: Catalytic Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ILV2, SMR1, YMR108W, YM9718.07 / Plasmid: pET30(c) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07342, acetolactate synthase

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Non-polymers , 8 types, 925 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-1TB / METHYL 2-[4-METHOXY-6-METHYL-1,3,5-TRAZIN-2-YL(METHYL)CARBAMOYLSULFAMOYL]BENZOATE / TRIBENURON METHYL


Mass: 395.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O6S
#5: Chemical ChemComp-YF3 / 2-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}PROPANE-1-THIOL


Mass: 212.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N4S
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-P23 / PROPYL TRIHYDROGEN DIPHOSPHATE


Mass: 220.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H10O7P2
#8: Chemical ChemComp-YF4 / 5-{[ETHYL(METHYL)AMINO]METHYL}-2-METHYL-5,6-DIHYDROPYRIMIDIN-4-AMINE


Mass: 180.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 3.53 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: potassium phosphate, thiamin diphosphate, FAD, magnesium chloride, DTT, tribenuron methyl, Tris-HCl, Lithium sulfate, sodium potassium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2002 / Details: mirrors
RadiationMonochromator: GE (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.58→99 Å / Num. obs: 67083 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.72 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.6
Reflection shellResolution: 2.58→2.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.95 / Num. unique all: 5303 / % possible all: 78.8

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Processing

Software
NameVersionClassification
Adxvdata processing
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N0H

1n0h


Resolution: 2.59→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 6631 -RANDOM
Rwork0.156 ---
obs0.16 65263 95.1 %-
all-67083 --
Displacement parametersBiso mean: 51.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.268 Å0.216 Å
Luzzati d res low-5 Å
Luzzati sigma a0.261 Å0.207 Å
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9059 0 215 913 10187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.157
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 2.59→2.69 Å
RfactorNum. reflection% reflection
Rfree0.233 614 -
Rwork0.193 --
obs-6074 79 %

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