8V3N

CCP5 in complex with Glu-P-Glu transition state analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Tubulin code eraser CCP5 binds branch glutamates by substrate deformation.

Chen, J.Zehr, E.A.Gruschus, J.M.Szyk, A.Liu, Y.Tanner, M.E.Tjandra, N.Roll-Mecak, A.

(2024) Nature 631: 905-912

  • DOI: https://doi.org/10.1038/s41586-024-07699-0
  • Primary Citation of Related Structures:  
    8V3M, 8V3N, 8V3O, 8V3P, 8V3Q, 8V3R, 8V3S, 8V4K, 8V4L, 8V4M

  • PubMed Abstract: 

    Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes 1 . Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification 2 . It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family 1 . Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function 3-9 , and mutations in CCPs lead to human disease 10-13 . 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.


  • Organizational Affiliation

    Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic carboxypeptidase-like protein 5524Homo sapiensMutation(s): 1 
Gene Names: AGBL5CCP5
EC: 3.4.17 (PDB Primary Data), 3.4.17.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NDL9 (Homo sapiens)
Explore Q8NDL9 
Go to UniProtKB:  Q8NDL9
PHAROS:  Q8NDL9
GTEx:  ENSG00000084693 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NDL9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.114α = 90
b = 80.414β = 90
c = 103.229γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States1ZIANS003163

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references
  • Version 1.2: 2024-08-07
    Changes: Database references