8V3S
Structure of CCP5 class3
Summary for 8V3S
| Entry DOI | 10.2210/pdb8v3s/pdb |
| EMDB information | 42952 |
| Descriptor | Cytosolic carboxypeptidase-like protein 5, beta tubulin tail, ZINC ION, ... (4 entities in total) |
| Functional Keywords | carboxypeptidase deglutamylation branch glutamate removal microtubule, hydrolase, hydrolase-substrate complex, hydrolase/substrate |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 2 |
| Total formula weight | 68929.63 |
| Authors | Chen, J.,Zehr, E.A.,Gruschus, J.M.,Szyk, A.,Liu, Y.,Tanner, M.E.,Tjandra, N.,Roll-Mecak, A. (deposition date: 2023-11-28, release date: 2024-07-17, Last modification date: 2024-11-06) |
| Primary citation | Chen, J.,Zehr, E.A.,Gruschus, J.M.,Szyk, A.,Liu, Y.,Tanner, M.E.,Tjandra, N.,Roll-Mecak, A. Tubulin code eraser CCP5 binds branch glutamates by substrate deformation. Nature, 631:905-912, 2024 Cited by PubMed Abstract: Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function, and mutations in CCPs lead to human disease. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax. PubMed: 39020174DOI: 10.1038/s41586-024-07699-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.6 Å) |
Structure validation
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