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- PDB-3pgq: Crystal Structure of the Carboxyltransferase Domain of S. cerevis... -

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Basic information

Entry
Database: PDB / ID: 3pgq
TitleCrystal Structure of the Carboxyltransferase Domain of S. cerevisiae Acetyl CoA Carboxylase in Complex with Pinoxaden
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE / Transferase / carboxyltransferase
Function / homology
Function and homology information


: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / long-chain fatty acid biosynthetic process / protein import into nucleus / fatty acid biosynthetic process / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal ...ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-GY3 / Acetyl-CoA carboxylase / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsTong, L. / Yu, L.P.C. / Kim, Y.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by pinoxaden.
Authors: Yu, L.P. / Kim, Y.S. / Tong, L.
History
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,0626
Polymers260,1193
Non-polymers9433
Water0
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0414
Polymers173,4132
Non-polymers6292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11460 Å2
ΔGint-93 kcal/mol
Surface area58370 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0414
Polymers173,4132
Non-polymers6292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-94 kcal/mol
Surface area56290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.180, 123.415, 145.711
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acetyl-CoA carboxylase / / ACC / Biotin carboxylase


Mass: 86706.359 Da / Num. of mol.: 3 / Fragment: UNP residues 1480-2195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FAS3, ACC1, YNR016C, N3175 / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: D6W1J1, UniProt: Q00955*PLUS, acetyl-CoA carboxylase
#2: Chemical ChemComp-GY3 / 8-(2-ethenyl-6-ethyl-4-methylphenyl)tetrahydro-7H-pyrazolo[1,2-d][1,4,5]oxadiazepine-7,9(8H)-dione


Mass: 314.379 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22N2O3
Nonpolymer detailsTHE STRUCTURE OF THE PINOXADEN IN THIS STRUCTURE IS THE HYDROLYZED, ACTIVE FORM

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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: 4.55 Å3/Da / Density % sol: 72.97 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 9% PEG8000, 0.1M sodium citrate pH 5.5, 10% glycerol, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 106428 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.8-2.94.40.43898.9
2.9-3.024.40.3398.4
3.02-3.154.50.25598.9
3.15-3.324.50.19499.2
3.32-3.534.60.14499.6
3.53-3.84.70.11699.9
3.8-4.184.80.09899.9
4.18-4.784.90.08299.7
4.78-6.024.90.07499.9
6.02-3050.0798.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.804 / SU ML: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING. THE AVERAGE TEMPERATURE FACTOR VALUES OF THE THREE INHIBITOR MOLECULES ARE 70, 74, AND 94 A2, WHILE THAT FOR ALL THREE PROTEIN MOLECULES IS 33 A2. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING. THE AVERAGE TEMPERATURE FACTOR VALUES OF THE THREE INHIBITOR MOLECULES ARE 70, 74, AND 94 A2, WHILE THAT FOR ALL THREE PROTEIN MOLECULES IS 33 A2. THIS SUGGESTS THAT THE OCCUPANCY OF THE INHIBITOR MAY NOT BE 100% IN THE CRYSTAL, ESPECIALLY FOR CHAIN C. THE LOWER OCCUPANCY IS ALSO CONSISTENT WITH OUR KINETIC STUDIES, WHICH SHOWED ONLY MINOR INHIBITION OF THE CT DOMAIN OF YEAST ACC BY PINOXADEN AT 1-MM CONCENTRATION
RfactorNum. reflection% reflection
Rfree0.239 5269 5 %
Rwork0.197 --
obs0.199 105743 98.4 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 107.48 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å20 Å20.07 Å2
2--6.37 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16299 0 69 0 16368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.96122678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.42252037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31523.81811
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.11152865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.76315136
X-RAY DIFFRACTIONr_chiral_restr0.1070.22444
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02112844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5121.510138
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.687216376
X-RAY DIFFRACTIONr_scbond_it4.38936599
X-RAY DIFFRACTIONr_scangle_it6.774.56302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.373 376 -
Rwork0.313 6975 -
obs--93.46 %
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)
11.4189-0.0930.08410.7396-0.32662.3624-0.02590.00510.1749-0.05460.0731-0.0449-0.1506-0.0499-0.04720.063-0.0494-0.02690.0847-0.01240.297613.017217.9932-4.3916
21.4323-0.20010.01811.4120.17973.04050.0264-0.01090.05240.1137-0.01220.14150.0945-0.0572-0.01420.0850.04640.0060.0953-0.00320.228844.9339-20.293936.4282
31.6723-0.1753-0.44981.18220.05852.7590.0119-0.1306-0.21430.1773-0.03520.04860.1451-0.12670.02330.22640.0225-0.00880.03610.050.237160.4932-40.877445.5508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1482 - 2195
2X-RAY DIFFRACTION2B1482 - 2195
3X-RAY DIFFRACTION3C1482 - 2195

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