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- PDB-1w93: Crystal Structure of Biotin Carboxylase Domain of Acetyl-Coenzyme... -

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Basic information

Entry
Database: PDB / ID: 1w93
TitleCrystal Structure of Biotin Carboxylase Domain of Acetyl-Coenzyme A Carboxylase from Saccharomyces cerevisiae
ComponentsACETYL-COENZYME A CARBOXYLASE
KeywordsLIGASE / OBESITY / DIABETES / FATTY ACID METABOLISM / STRUCTURE-BASED DRUG DESIGN / ALLOSTERIC INHIBITION / POLYKETIDE
Function / homology
Function and homology information


Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase / 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 / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / 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
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 / Biotin-binding site / Biotin-requiring enzymes attachment site. / 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
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShen, Y. / Volrath, S.L. / Weatherly, S.C. / Elich, T.D. / Tong, L.
CitationJournal: Mol.Cell / Year: 2004
Title: A Mechanism for the Potent Inhibition of Eukaryotic Acetyl-Coenzyme a Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product
Authors: Shen, Y. / Volrath, S.L. / Weatherly, S.C. / Elich, T.D. / Tong, L.
History
DepositionOct 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYL-COENZYME A CARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)61,5231
Polymers61,5231
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.740, 101.740, 145.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein ACETYL-COENZYME A CARBOXYLASE / ACC


Mass: 61523.172 Da / Num. of mol.: 1 / Fragment: BIOTIN CARBOXYLASE DOMAIN, RESIDUES 14-566
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00955, acetyl-CoA carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97931
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 24971 / % possible obs: 84.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / % possible all: 57.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKLdata reduction
HKLdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.63 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 153597.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.323 1732 6.9 %RANDOM
Rwork0.254 ---
obs0.254 24971 84.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 136.81 Å2 / ksol: 0.338662 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.01 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-
Refinement stepCycle: LAST / Resolution: 2.5→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 0 149 4438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.412.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.297 126 7.4 %
Rwork0.259 1575 -
obs--57.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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