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Yorodumi- PDB-7ebc: Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ebc | ||||||
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Title | Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae | ||||||
Components | Isocitrate lyase | ||||||
Keywords | LYASE / Isocitrate lyase / glyoxylate cycle / ubiquitination | ||||||
Function / homology | Function and homology information methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / vacuole / tricarboxylic acid cycle / extracellular region / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hiragi, K. / Nishio, K. / Moriyama, S. / Hamaguchi, T. / Mizoguchi, A. / Yonekura, K. / Tani, K. / Mizushima, T. | ||||||
Citation | Journal: J Struct Biol / Year: 2021 Title: Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase. Authors: Keito Hiragi / Kazuya Nishio / Shu Moriyama / Tasuku Hamaguchi / Akira Mizoguchi / Koji Yonekura / Kazutoshi Tani / Tsunehiro Mizushima / Abstract: In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique ...In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique step of the cycle. The ICL of S.cerevisiae (ScIcl1) is tagged for proteasomal degradation through ubiquitination by a multisubunit ubiquitin ligase (the glucose-induced degradation-deficient (GID) complex), whereas that of the pathogenic yeast Candida albicans (CaIcl1) escapes this process. However, the reason for the ubiquitin targeting specificity of the GID complex for ScIcl1 and not for CaIcl1 is unclear. To gain some insight into this, in this study, the crystal structures of apo ScIcl1 and CaIcl1 in complex with formate and the cryogenic electron microscopy structure of apo CaIcl1 were determined at a resolution of 2.3, 2.7, and 2.6 Å, respectively. A comparison of the various structures suggests that the orientation of N-terminal helix α1 in S.cerevisiae is likely key to repositioning of ubiquitination sites and contributes to the distinction found in C. albicans ubiquitin evasion mechanism. This finding gives us a better understanding of the molecular mechanism of ubiquitin-dependent ScIcl1 degradation and could serve as a theoretical basis for the research and development of anti-C. albicans drugs based on the concept of CaIcl1 ubiquitination. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ebc.cif.gz | 425.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebc.ent.gz | 345 KB | Display | PDB format |
PDBx/mmJSON format | 7ebc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebc ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebc | HTTPS FTP |
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-Related structure data
Related structure data | 7ebeC 7ebfC 5e9gS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 63320.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P28240, isocitrate lyase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.75 Å3/Da / Density % sol: 55.24 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 40mM Na-HEPES pH7.0, 8%(w/v)PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.9 Å / Num. obs: 116065 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 11263 / CC1/2: 0.788 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E9G Resolution: 2.3→48.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.539 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.349 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→48.8 Å
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Refine LS restraints |
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