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Yorodumi- PDB-6l1q: Crystal structure of AfCbbQ2, a MoxR AAA+-ATPase and CbbQO-type R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l1q | ||||||
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Title | Crystal structure of AfCbbQ2, a MoxR AAA+-ATPase and CbbQO-type Rubisco activase from Acidithiobacillus ferrooxidans | ||||||
Components | CbbQ protein | ||||||
Keywords | CHAPERONE / AAA+ ATPase / cbbQO-type rubisco activase / MoxR family / Molecular chaperone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acidithiobacillus ferrooxidans ATCC 23270 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ye, F.Z. / Tsai, Y.C.C. / Mueller-Cajar, O. / Gao, Y.G. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Insights into the mechanism and regulation of the CbbQO-type Rubisco activase, a MoxR AAA+ ATPase. Authors: Yi-Chin Candace Tsai / Fuzhou Ye / Lynette Liew / Di Liu / Shashi Bhushan / Yong-Gui Gao / Oliver Mueller-Cajar / Abstract: The vast majority of biological carbon dioxide fixation relies on the function of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). In most cases the enzyme exhibits a tendency to become ...The vast majority of biological carbon dioxide fixation relies on the function of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). In most cases the enzyme exhibits a tendency to become inhibited by its substrate RuBP and other sugar phosphates. The inhibition is counteracted by diverse molecular chaperones known as Rubisco activases (Rcas). In some chemoautotrophic bacteria, the CbbQO-type Rca Q2O2 repairs inhibited active sites of hexameric form II Rubisco. The 2.2-Å crystal structure of the MoxR AAA+ protein CbbQ2 from reveals the helix 2 insert (H2I) that is critical for Rca function and forms the axial pore of the CbbQ hexamer. Negative-stain electron microscopy shows that the essential CbbO adaptor protein binds to the conserved, concave side of the CbbQ2 hexamer. Site-directed mutagenesis supports a model in which adenosine 5'-triphosphate (ATP)-powered movements of the H2I are transmitted to CbbO via the concave residue L85. The basal ATPase activity of Q2O2 Rca is repressed but strongly stimulated by inhibited Rubisco. The characterization of multiple variants where this repression is released indicates that binding of inhibited Rubisco to the C-terminal CbbO VWA domain initiates a signal toward the CbbQ active site that is propagated via elements that include the CbbQ α4-β4 loop, pore loop 1, and the presensor 1-β hairpin (PS1-βH). Detailed mechanistic insights into the enzyme repair chaperones of the highly diverse CO fixation machinery of Proteobacteria will facilitate their successful implementation in synthetic biology ventures. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l1q.cif.gz | 328.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l1q.ent.gz | 260.2 KB | Display | PDB format |
PDBx/mmJSON format | 6l1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l1q_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6l1q_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6l1q_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 6l1q_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/6l1q ftp://data.pdbj.org/pub/pdb/validation_reports/l1/6l1q | HTTPS FTP |
-Related structure data
Related structure data | 0789C 5c3cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41976.648 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria) Strain: ATCC 23270 / Gene: cbbQ-2, AFE_2156 / Plasmid: pOPThisLipo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7J5E4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 21.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: 25% (v/v) 1,2-propanediol, phosphate-citrate pH4.2, 5% (v/v) PEG3000, 10% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.05 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 56135 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 8038 / CC1/2: 0.95 / Rpim(I) all: 0.18 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5c3c Resolution: 2.2→29.056 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.6 / Stereochemistry target values: ML Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.71 Å2 / Biso mean: 37.7988 Å2 / Biso min: 13.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→29.056 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 6.8442 Å / Origin y: 57.6726 Å / Origin z: 4.3962 Å
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Refinement TLS group |
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