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- PDB-3n6r: CRYSTAL STRUCTURE OF the holoenzyme of PROPIONYL-COA CARBOXYLASE (PCC) -

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Basic information

Entry
Database: PDB / ID: 3n6r
TitleCRYSTAL STRUCTURE OF the holoenzyme of PROPIONYL-COA CARBOXYLASE (PCC)
Components
  • Propionyl-CoA carboxylase, alpha subunit
  • Propionyl-CoA carboxylase, beta subunit
KeywordsLIGASE / protein complex / biotin-dependent carboxylase
Function / homology
Function and homology information


propionate metabolic process / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / lipid catabolic process / ATP binding / metal ion binding
Similarity search - Function
Glycoprotein, Type 4 Pilin - #30 / Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / Glycoprotein, Type 4 Pilin / 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 ...Glycoprotein, Type 4 Pilin - #30 / Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / Glycoprotein, Type 4 Pilin / 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 / Rossmann fold - #20 / 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 / ATP-grasp fold, A domain / 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, 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-BTI / Propionyl-CoA carboxylase beta chain / Propionyl-CoA carboxylase alpha chain
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
Roseobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHuang, C.S. / Sadre-Bazzaz, K. / Tong, L.
CitationJournal: Nature / Year: 2010
Title: Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.
Authors: Christine S Huang / Kianoush Sadre-Bazzaz / Yang Shen / Binbin Deng / Z Hong Zhou / Liang Tong /
Abstract: Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd ...Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd number of carbon atoms. Deficiencies in PCC activity in humans are linked to the disease propionic acidaemia, an autosomal recessive disorder that can be fatal in infants. The holoenzyme of PCC is an alpha(6)beta(6) dodecamer, with a molecular mass of 750 kDa. The alpha-subunit contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains, whereas the beta-subunit supplies the carboxyltransferase (CT) activity. Here we report the crystal structure at 3.2-A resolution of a bacterial PCC alpha(6)beta(6) holoenzyme as well as cryo-electron microscopy (cryo-EM) reconstruction at 15-A resolution demonstrating a similar structure for human PCC. The structure defines the overall architecture of PCC and reveals unexpectedly that the alpha-subunits are arranged as monomers in the holoenzyme, decorating a central beta(6) hexamer. A hitherto unrecognized domain in the alpha-subunit, formed by residues between the BC and BCCP domains, is crucial for interactions with the beta-subunit. We have named it the BT domain. The structure reveals for the first time the relative positions of the BC and CT active sites in the holoenzyme. They are separated by approximately 55 A, indicating that the entire BCCP domain must translocate during catalysis. The BCCP domain is located in the active site of the beta-subunit in the current structure, providing insight for its involvement in the CT reaction. The structural information establishes a molecular basis for understanding the large collection of disease-causing mutations in PCC and is relevant for the holoenzymes of other biotin-dependent carboxylases, including 3-methylcrotonyl-CoA carboxylase (MCC) and eukaryotic acetyl-CoA carboxylase (ACC).
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Propionyl-CoA carboxylase, alpha subunit
B: Propionyl-CoA carboxylase, beta subunit
C: Propionyl-CoA carboxylase, alpha subunit
D: Propionyl-CoA carboxylase, beta subunit
E: Propionyl-CoA carboxylase, alpha subunit
F: Propionyl-CoA carboxylase, beta subunit
G: Propionyl-CoA carboxylase, alpha subunit
H: Propionyl-CoA carboxylase, beta subunit
I: Propionyl-CoA carboxylase, alpha subunit
J: Propionyl-CoA carboxylase, beta subunit
K: Propionyl-CoA carboxylase, alpha subunit
L: Propionyl-CoA carboxylase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)795,86218
Polymers794,49212
Non-polymers1,3706
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area73220 Å2
ΔGint-286 kcal/mol
Surface area237170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.890, 159.170, 153.740
Angle α, β, γ (deg.)113.87, 101.03, 108.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Propionyl-CoA carboxylase, alpha subunit


Mass: 73946.180 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Gene: pccA, SPO1101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LUF3, propionyl-CoA carboxylase
#2: Protein
Propionyl-CoA carboxylase, beta subunit


Mass: 58469.172 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseobacter denitrificans (bacteria) / Strain: OCh 114 / Gene: pccB, RD1_2028 / Production host: Escherichia coli (E. coli) / References: UniProt: Q168G2, propionyl-CoA carboxylase
#3: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O2S

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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: 3.37 Å3/Da / Density % sol: 63.53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 169648 / % possible obs: 92 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.6854
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.024 / % possible all: 80

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29.36 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 194743.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE RESIDUES ARE NUMBERED ACCORDING TO THE HUMAN PCC SEQUENCE
RfactorNum. reflection% reflectionSelection details
Rfree0.245 11579 7.5 %RANDOM
Rwork0.212 ---
obs0.212 155003 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.3531 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å21.03 Å2-4.3 Å2
2---1.42 Å2-8.64 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51831 0 90 0 51921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 1038 7.7 %
Rwork0.319 12393 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2bti.par

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