8V4L

CCP5 in complex with microtubules class2

Summary for 8V4L

• Entry DOI: 10.2210/pdb8v4l/pdb
• EMDB information: 42972
• Descriptor: Tubulin alpha-1B chain, Tubulin beta chain, Cytosolic carboxypeptidase-like protein 5, ... (8 entities in total)
• Functional Keywords: carboxypeptidase deglutamylation branch glutamate removal microtubule, hydrolase, hydrolase-substrate complex, hydrolase-substrate, structural protein complex, hydrolase/substrate, structural protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 271791.59

Authors

Chen, J.,Zehr, E.A.,Gruschus, J.M.,Szyk, A.,Liu, Y.,Tanner, M.E.,Tjandra, N.,Roll-Mecak, A. (deposition date: 2023-11-29, release date: 2024-07-17, Last modification date: 2024-10-23)

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

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: 39020174
DOI: 10.1038/s41586-024-07699-0

Experimental method

ELECTRON MICROSCOPY (2.9 Å)