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Yorodumi- PDB-6h7g: Crystal structure of redox-sensitive phosphoribulokinase (PRK) fr... -
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-Basic information
Entry | Database: PDB / ID: 6h7g | ||||||
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Title | Crystal structure of redox-sensitive phosphoribulokinase (PRK) from the green algae Chlamydomonas reinhardtii | ||||||
Components | Phosphoribulokinase, chloroplastic | ||||||
Keywords | PHOTOSYNTHESIS / Transferase / ATP binding / kinase activity | ||||||
Function / homology | Function and homology information phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / phosphorylation / enzyme binding ...phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / phosphorylation / enzyme binding / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fermani, S. / Sparla, F. / Gurrieri, L. / Demitri, N. / Polentarutti, M. / Falini, G. / Trost, P. / Lemaire, S.D. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: and phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle. Authors: Libero Gurrieri / Alessandra Del Giudice / Nicola Demitri / Giuseppe Falini / Nicolae Viorel Pavel / Mirko Zaffagnini / Maurizio Polentarutti / Pierre Crozet / Christophe H Marchand / Julien ...Authors: Libero Gurrieri / Alessandra Del Giudice / Nicola Demitri / Giuseppe Falini / Nicolae Viorel Pavel / Mirko Zaffagnini / Maurizio Polentarutti / Pierre Crozet / Christophe H Marchand / Julien Henri / Paolo Trost / Stéphane D Lemaire / Francesca Sparla / Simona Fermani / Abstract: In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known ...In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga (PRK) and the land plant (PRK). PRK is an elongated homodimer characterized by a large central β-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes-the clamp loop-which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both PRK and PRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h7g.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h7g.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 6h7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/6h7g ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h7g | HTTPS FTP |
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-Related structure data
Related structure data | 6h7hC 5b3fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38813.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PRKA / Organ: chloroplast / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19824, phosphoribulokinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: needle-like |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 22 % w/v PEG MME 5K, 0.1 M MES, pH 6.5, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.24 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2015 |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.38 Å / Num. obs: 27230 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3280 / CC1/2: 0.743 / Rsym value: 0.77 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B3F Resolution: 2.6→39.859 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.859 Å
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Refine LS restraints |
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LS refinement shell |
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