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- PDB-3h0q: Crystal structure of the carboxyltransferase domain of acetyl-coe... -

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Basic information

Entry
Database: PDB / ID: 3h0q
TitleCrystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with compound 3
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE / TRANSFERASE / ACETYL-COA CARBOXYLASE / CARBOXYLTRANSFERASE / INHIBITOR
Function / homology
Function and homology information


Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / 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 / metal ion binding / identical protein 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-B37 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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)263,1296
Polymers261,7143
Non-polymers1,4153
Water12,322684
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4194
Polymers174,4762
Non-polymers9432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12090 Å2
ΔGint-98 kcal/mol
Surface area55030 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4194
Polymers174,4762
Non-polymers9432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-99 kcal/mol
Surface area52800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.953, 124.248, 145.271
Angle α, β, γ (deg.)90.000, 94.229, 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-B37 / 4-({4-[(2-methylquinolin-6-yl)methyl]piperidin-1-yl}carbonyl)-2-phenylquinoline / [4-(2-Methyl-quinolin-6-ylmethyl)-piperidin-1-yl]-(2-phenyl-quinolin-4-yl)-methanon


Mass: 471.592 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H29N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 4.25 Å3/Da / Density % sol: 71.03 %
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

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→48.72 Å / Num. obs: 146153 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.129 / Χ2: 1.358 / Net I/σ(I): 7.58
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.593.80.402144441.38598.4
2.59-2.693.80.333144831.67298.5
2.69-2.823.80.273144741.70698.6
2.82-2.963.80.225145971.82598.8
2.96-3.153.80.192145661.54398.9
3.15-3.393.80.168145871.50199
3.39-3.733.80.149146831.02399.2
3.73-4.273.80.13147080.95499.3
4.27-5.383.80.109147351.13499.4
5.38-503.80.074148760.8598.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.72 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.233 7227 4.8 %
Rwork0.205 --
obs-146091 96.6 %
Displacement parametersBiso max: 126.91 Å2 / Biso mean: 50.447 Å2 / Biso min: 21.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.101 Å20 Å20.096 Å2
2---0.213 Å20 Å2
3---0.112 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16098 0 108 684 16890
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3281.5
X-RAY DIFFRACTIONc_scbond_it1.9682
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scangle_it2.8272.5
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 DIFFRACTION5PF03390473.par

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