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- PDB-2kcc: Solution Structure of biotinoyl domain from human acetyl-CoA carb... -

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Basic information

Entry
Database: PDB / ID: 2kcc
TitleSolution Structure of biotinoyl domain from human acetyl-CoA carboxylase 2
ComponentsAcetyl-CoA carboxylase 2
KeywordsLIGASE / acetyl-CoA carboxylase / biotinoyl domain / BCCP / BirA / biotinylation / 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 / acetyl-CoA metabolic process / tricarboxylic acid 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 / acetyl-CoA metabolic process / tricarboxylic acid 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 metabolism / biotin binding / 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 / metal ion binding / nucleus / cytosol
Similarity search - Function
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 ...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 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Acetyl-CoA carboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLee, C. / Cheong, H. / Ryu, K. / Lee, J. / Lee, W. / Jeon, Y. / Cheong, C.
CitationJournal: Proteins / Year: 2008
Title: Biotinoyl domain of human acetyl-CoA carboxylase: Structural insights into the carboxyl transfer mechanism.
Authors: Lee, C.K. / Cheong, H.K. / Ryu, K.S. / Lee, J.I. / Lee, W. / Jeon, Y.H. / Cheong, C.
History
DepositionDec 19, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Sep 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)9,4241
Polymers9,4241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 9423.708 Da / Num. of mol.: 1 / Fragment: biotinoyl domain, residues 891-964
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACACB, ACC2, ACCB / Production host: Escherichia coli (E. coli)
References: UniProt: O00763, acetyl-CoA carboxylase, biotin carboxylase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 50 mM HEPES-1, 1 mM DTT-2, 150 mM sodium chloride-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMHEPES-11
1 mMDTT-21
150 mMsodium chloride-31
Sample conditionsIonic strength: 0.05 / pH: 7.3 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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