6OCF

The crystal structure of VASH1-SVBP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of tubulin detyrosination by vasohibins.

Li, F.Hu, Y.Qi, S.Luo, X.Yu, H.

(2019) Nat.Struct.Mol.Biol. 26: 583-591

  • DOI: 10.1038/s41594-019-0242-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microtubules are regulated by post-translational modifications of tubulin. The ligation and cleavage of the carboxy-terminal tyrosine of α-tubulin impact microtubule functions during mitosis, cardiomyocyte contraction and neuronal processes. Tubulin ...

    Microtubules are regulated by post-translational modifications of tubulin. The ligation and cleavage of the carboxy-terminal tyrosine of α-tubulin impact microtubule functions during mitosis, cardiomyocyte contraction and neuronal processes. Tubulin tyrosination and detyrosination are mediated by tubulin tyrosine ligase and the recently discovered tubulin detyrosinases, vasohibin 1 and 2 (VASH1 and VASH2) bound to the small vasohibin-binding protein (SVBP). Here, we report the crystal structures of human VASH1-SVBP alone, in complex with a tyrosine-derived covalent inhibitor and bound to the natural product parthenolide. The structures and subsequent mutagenesis analyses explain the requirement for SVBP during tubulin detyrosination, and reveal the basis for the recognition of the C-terminal tyrosine and the acidic α-tubulin tail by VASH1. The VASH1-SVBP-parthenolide structure provides a framework for designing more effective chemical inhibitors of vasohibins, which can be valuable for dissecting their biological functions and may have therapeutic potential.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. Hongtao.Yu@utsouthwestern.edu.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuelian.Luo@utsouthwestern.edu.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuelian.Luo@utsouthwestern.edu.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Hongtao.Yu@utsouthwestern.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulinyl-Tyr carboxypeptidase 1
A
248Homo sapiensMutation(s): 0 
Gene Names: VASH1 (KIAA1036, VASH)
EC: 3.4.17.17
Find proteins for Q7L8A9 (Homo sapiens)
Go to Gene View: VASH1
Go to UniProtKB:  Q7L8A9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small vasohibin-binding protein
B
49Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 100.558α = 90.00
b = 100.558β = 90.00
c = 206.730γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
HKL-3000data reduction
PHENIXrefinement
HKL-3000data collection
AutoSolphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-23 
  • Released Date: 2019-06-26 
  • Deposition Author(s): Li, F., Luo, X., Yu, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesRP150538-P2

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence