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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31053 | |||||||||
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Title | Cryo-EM structure of Isocitrate lyase-1 from Candida albicans | |||||||||
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![]() | Isocitrate lyase / glyoxylate cycle / ubiquitination / LYASE | |||||||||
Function / homology | ![]() methylisocitrate lyase activity / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / peroxisome / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.63 Å | |||||||||
![]() | Hiragi K / Nishio K | |||||||||
![]() | ![]() 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 116.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.3 KB 9.3 KB | Display Display | ![]() |
Images | ![]() | 86.3 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ebfMC ![]() 7ebcC ![]() 7ebeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.823 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Isocitrate lyase
Entire | Name: Isocitrate lyase |
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Components |
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-Supramolecule #1: Isocitrate lyase
Supramolecule | Name: Isocitrate lyase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Isocitrate lyase
Macromolecule | Name: Isocitrate lyase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: isocitrate lyase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 62.336523 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: HHHHHHMPYT PIDIQKEEAD FQKEVAEIKK WWSEPRWRKT KRIYSAEDIA KKRGTLKINH PSSQQADKLF KLLEKHDADK TVSFTFGAL DPIHVAQMAK YLDSIYVSGW QCSSTASTSN EPSPDLADYP MDTVPNKVEH LWFAQLFHDR KQREERLTLS K EERAKTPY ...String: HHHHHHMPYT PIDIQKEEAD FQKEVAEIKK WWSEPRWRKT KRIYSAEDIA KKRGTLKINH PSSQQADKLF KLLEKHDADK TVSFTFGAL DPIHVAQMAK YLDSIYVSGW QCSSTASTSN EPSPDLADYP MDTVPNKVEH LWFAQLFHDR KQREERLTLS K EERAKTPY IDFLRPIIAD ADTGHGGITA IIKLTKMFIE RGAAGIHIED QAPGTKKCGH MAGKVLVPVQ EHINRLVAIR AS ADIFGSN LLAVARTDSE AATLITSTID HRDHYFIIGA TNPEAGDLAA LMAEAESKGI YGNELAAIES EWTKKAGLKL FHE AVIDEI KNGNYSNKDA LIKKFTDKVN PLSHTSHKEA KKLAKELTGK DIYFNWDVAR AREGYYRYQG GTQCAVMRGR AFAP YADLI WMESALPDYA QAKEFADGVK AAVPDQWLAY NLSPSFNWNK AMPADEQETY IKRLGKLGYV WQFITLAGLH TTALA VDDF SNQYSQIGMK AYGQTVQQPE IEKGVEVVKH QKWSGATYID GLLKMVSGGV TSTAAMGQGV TEDQFKESKA KA UniProtKB: Isocitrate lyase |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 42.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179026 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |