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- PDB-3h0j: Crystal structure of the carboxyltransferase domain of acetyl-coe... -

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Basic information

Entry
Database: PDB / ID: 3h0j
TitleCrystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with compound 2
ComponentsAcetyl-CoA carboxylase
KeywordsTRANSFERASE / ACETYL-COA CARBOXYLASE / CARBOXYLTRANSFERASE / INHIBITOR / ACC / CT / ATP-binding / Biotin / Cytoplasm / Fatty acid biosynthesis / Ligase / Lipid synthesis / Metal-binding / Multifunctional enzyme / Nucleotide-binding
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 / fatty acid biosynthetic process / protein import into nucleus / 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-B36 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, H. / Tong, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Discovery of small molecule isozyme non-specific inhibitors of mammalian acetyl-CoA carboxylase 1 and 2.
Authors: Corbett, J.W. / Freeman-Cook, K.D. / Elliott, R. / Vajdos, F. / Rajamohan, F. / Kohls, D. / Marr, E. / Zhang, H. / Tong, L. / Tu, M. / Murdande, S. / Doran, S.D. / Houser, J.A. / Song, W. / ...Authors: Corbett, J.W. / Freeman-Cook, K.D. / Elliott, R. / Vajdos, F. / Rajamohan, F. / Kohls, D. / Marr, E. / Zhang, H. / Tong, L. / Tu, M. / Murdande, S. / Doran, S.D. / Houser, J.A. / Song, W. / Jones, C.J. / Coffey, S.B. / Buzon, L. / Minich, M.L. / Dirico, K.J. / Tapley, S. / McPherson, R.K. / Sugarman, E. / Harwood, H.J. / Esler, W.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,0486
Polymers261,7143
Non-polymers1,3343
Water00
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3654
Polymers174,4762
Non-polymers8892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11810 Å2
ΔGint-96 kcal/mol
Surface area56100 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3654
Polymers174,4762
Non-polymers8892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-100 kcal/mol
Surface area53370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.736, 122.865, 145.885
Angle α, β, γ (deg.)90.000, 93.918, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 87237.977 Da / Num. of mol.: 3 / Fragment: Residues 1476-2233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FAS3, ACC1, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-B36 / 6-{[1-(anthracen-9-ylcarbonyl)piperidin-4-yl]methyl}-2-methylquinoline / Anthracen-9-yl-[4-(2-methyl-quinolin-6-ylmethyl)-piperidin-1-yl]-methanon


Mass: 444.567 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H28N2O

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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: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M Na citrate, pH 5.5, 200 mM NaCl, 8% PEG8000, 10% glycerol, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→51.25 Å / Num. obs: 106688 / % possible obs: 99.7 % / Redundancy: 3.67 % / Rmerge(I) obs: 0.087 / Χ2: 0.99 / Scaling rejects: 2959
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.8-2.93.590.3113.937718104581.198.3
2.9-3.023.670.2824.139096106091.05100
3.02-3.153.680.2424.639359106751.05100
3.15-3.323.680.2075.139356106591.04100
3.32-3.533.680.1536.439558107011.01100
3.53-3.83.690.1098.439431106520.98100
3.8-4.183.70.08310.839792107050.95100
4.18-4.793.70.06114.639906107040.94100
4.79-6.033.710.05516.240210107540.89100
6.03-51.253.590.0392439926107710.998.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata processing
CNSrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→51.25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.819 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.257 5328 5 %
Rwork0.228 --
obs-106688 99.7 %
Displacement parametersBiso max: 133.39 Å2 / Biso mean: 52.547 Å2 / Biso min: 15.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.147 Å20 Å20.011 Å2
2---0.224 Å20 Å2
3---0.077 Å2
Refinement stepCycle: LAST / Resolution: 2.8→51.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16098 0 102 0 16200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2461.5
X-RAY DIFFRACTIONc_scbond_it1.6732
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scangle_it2.6242.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5PF03324646_eq.par

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