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- PDB-3jrw: Phosphorylated BC domain of ACC2 -

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Basic information

Entry
Database: PDB / ID: 3jrw
TitlePhosphorylated BC domain of ACC2
ComponentsAcetyl-CoA carboxylase 2
KeywordsLIGASE / BC DOMAIN / PHOSPHORYLATION / Alternative splicing / ATP-binding / Biotin / Fatty acid biosynthesis / Lipid synthesis / Manganese / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


intracellular aspartate homeostasis / lactic acid secretion / mitochondrial fatty acid beta-oxidation multienzyme complex / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of heart growth / acetyl-CoA carboxylase / Biotin transport and metabolism / negative regulation of fatty acid beta-oxidation / tricarboxylic acid metabolic process / acetyl-CoA metabolic process ...intracellular aspartate homeostasis / lactic acid secretion / mitochondrial fatty acid beta-oxidation multienzyme complex / regulation of cardiac muscle hypertrophy in response to stress / positive regulation of heart growth / acetyl-CoA carboxylase / Biotin transport and metabolism / negative regulation of fatty acid beta-oxidation / tricarboxylic acid metabolic process / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / intracellular glutamate homeostasis / positive regulation of lipid storage / pentose-phosphate shunt / Carnitine shuttle / biotin binding / D-glucose import / fatty acid oxidation / regulation of glucose metabolic process / energy homeostasis / response to nutrient / Activation of gene expression by SREBF (SREBP) / response to organic cyclic compound / fatty acid biosynthetic process / protein homotetramerization / mitochondrial outer membrane / response to xenobiotic stimulus / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
PreATP-grasp fold / PreATP-grasp domain / 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 ...PreATP-grasp fold / PreATP-grasp domain / 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 / Rossmann fold - #20 / 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 / ATP-grasp fold, A domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl-CoA carboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCho, Y.S. / Lee, J.I. / Shin, D. / Kim, H.T. / Lee, T.G. / Heo, Y.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Molecular mechanism for the regulation of human ACC2 through phosphorylation by AMPK
Authors: Cho, Y.S. / Lee, J.I. / Shin, D. / Kim, H.T. / Jung, H.Y. / Lee, T.G. / Kang, L.W. / Ahn, Y.J. / Cho, H.S. / Heo, Y.S.
History
DepositionSep 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase 2


Theoretical massNumber of molelcules
Total (without water)65,5031
Polymers65,5031
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.740, 75.740, 189.474
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Acetyl-CoA carboxylase 2 / ACC-beta / Biotin carboxylase / ACC2


Mass: 65503.289 Da / Num. of mol.: 1 / Fragment: BC DOMAIN, RESIDUES 217-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACACB, ACC2, ACCB / Plasmid: MODIFIED PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O00763, acetyl-CoA carboxylase, biotin carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: AMMONIUM SULFATE, MES, pH 6.50, VAPOR DIFFUSION, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.6→50 Å / Num. all: 20057 / Num. obs: 18433 / % possible obs: 91.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.6 Å2
Reflection shellResolution: 2.6→2.7 Å / % possible all: 82.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hjw

2hjw


Resolution: 2.6→19.85 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 420924.64 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 898 4.9 %RANDOM
Rwork0.234 ---
all0.239 20057 --
obs0.234 18232 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.12 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 63 Å2
Baniso -1Baniso -2Baniso -3
1-14.71 Å213.04 Å20 Å2
2--14.71 Å20 Å2
3----29.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 0 53 3960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 147 5.2 %
Rwork0.386 2668 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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