6JZE

Crystal structure of VASH2-SVBP complex with the magic triangle I3C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer.

Zhou, C.Yan, L.Zhang, W.H.Liu, Z.

(2019) Nat Commun 10: 3212-3212

  • DOI: 10.1038/s41467-019-11277-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. liuzhu@mail.hzau.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulinyl-Tyr carboxypeptidase 2
A
313Mus musculusMutation(s): 0 
Gene Names: Vash2 (Vashl)
EC: 3.4.17.17
Find proteins for Q8C5G2 (Mus musculus)
Go to UniProtKB:  Q8C5G2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small vasohibin-binding protein
B
88Homo sapiensMutation(s): 0 
Gene Names: SVBP (CCDC23)
Find proteins for Q8N300 (Homo sapiens)
Go to Gene View: SVBP
Go to UniProtKB:  Q8N300
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3C
Query on I3C

Download SDF File 
Download CCD File 
A, B
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
5-Amino-2,4,6-triiodoisophthalic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
I3C
Query on I3C
A
NON-POLYMERC8 H4 I3 N O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.690α = 90.00
b = 111.115β = 90.00
c = 126.454γ = 90.00
Software Package:
Software NamePurpose
SHELXDEphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release