6JZD image
Deposition Date 2019-05-01
Release Date 2019-07-17
Last Version Date 2024-03-27
Entry Detail
PDB ID:
6JZD
Title:
Crystal structure of peptide-bound VASH2-SVBP complex
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.48 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Tubulinyl-Tyr carboxypeptidase 2
Gene (Uniprot):Vash2
Mutations:C158A
Chain IDs:A
Chain Length:355
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Small vasohibin-binding protein
Gene (Uniprot):SVBP
Chain IDs:B
Chain Length:88
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:GLU-GLY-GLU-GLU-TYR
Chain IDs:C
Chain Length:15
Number of Molecules:1
Biological Source:Mus musculus
Primary Citation
Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer.
Nat Commun 10 3212 3212 (2019)
PMID: 31324789 DOI: 10.1038/s41467-019-11277-8

Abstact

The C-terminus of α-tubulin undergoes a detyrosination/tyrosination cycle and dysregulation of this cycle is associated with cancer and other diseases. The molecular mechanisms of tubulin tyrosination are well studied, however it has remained unknown how tyrosine is cleaved from the tubulin tail. Here, we report the crystal structure of the long-sought detyrosination enzyme, the VASH2/SVBP heterodimer at 2.2 Å resolution and the structure of the tail/VASH2/SVBP complex at 2.5 Å resolution. VASH2 possesses a non-canonical Cys-His-Ser catalytic architecture for tyrosine cleavage. The dynamics of the α1- and α2- helices of VASH2 are related to the insolubility of VASH2. SVBP plays a chaperone-like role by extensively interacting with VASH2 and stabilizing these dynamic helices. A positively charged groove around the catalytic pocket and the α1- and α2- helices of VASH2 targets the tubulin tail for detyrosination. We provide insights into the mechanisms underlying the cycle of tubulin tyrosine cleavage and religation.

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