[English] 日本語
Yorodumi- PDB-3n6r: CRYSTAL STRUCTURE OF the holoenzyme of PROPIONYL-COA CARBOXYLASE (PCC) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n6r | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF the holoenzyme of PROPIONYL-COA CARBOXYLASE (PCC) | ||||||
Components |
| ||||||
Keywords | LIGASE / 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 | ||||||
Biological species | Ruegeria pomeroyi (bacteria) Roseobacter denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Huang, C.S. / Sadre-Bazzaz, K. / Tong, L. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3n6r.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3n6r.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 3n6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n6r_validation.pdf.gz | 614.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3n6r_full_validation.pdf.gz | 983.1 KB | Display | |
Data in XML | 3n6r_validation.xml.gz | 268.4 KB | Display | |
Data in CIF | 3n6r_validation.cif.gz | 358.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/3n6r ftp://data.pdbj.org/pub/pdb/validation_reports/n6/3n6r | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 | 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 / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.53 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.2→3.31 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.024 / % possible all: 80 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.3531 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→29.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|