6QBY

Crystal structure of VASH 2 in complex with SVBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex.

Wang, N.Bosc, C.Ryul Choi, S.Boulan, B.Peris, L.Olieric, N.Bao, H.Krichen, F.Chen, L.Andrieux, A.Olieric, V.Moutin, M.J.Steinmetz, M.O.Huang, H.

(2019) Nat Struct Mol Biol 26: 571-582

  • DOI: 10.1038/s41594-019-0241-y
  • Primary Citation of Related Structures:  
    6J4O, 6J4P, 6J4Q, 6J4S, 6J4U, 6J4V, 6QBY

  • PubMed Abstract: 
  • Vasohibins are tubulin tyrosine carboxypeptidases that are important in neuron physiology. We examined the crystal structures of human vasohibin 1 and 2 in complex with small vasohibin-binding protein (SVBP) in the absence and presence of different inhibitors and a C-terminal α-tubulin peptide ...

    Vasohibins are tubulin tyrosine carboxypeptidases that are important in neuron physiology. We examined the crystal structures of human vasohibin 1 and 2 in complex with small vasohibin-binding protein (SVBP) in the absence and presence of different inhibitors and a C-terminal α-tubulin peptide. In combination with functional data, we propose that SVBP acts as an activator of vasohibins. An extended groove and a distinctive surface residue patch of vasohibins define the specific determinants for recognizing and cleaving the C-terminal tyrosine of α-tubulin and for binding microtubules, respectively. The vasohibin-SVBP interaction and the ability of the enzyme complex to associate with microtubules regulate axon specification of neurons. Our results define the structural basis of tubulin detyrosination by vasohibins and show the relevance of this process for neuronal development. Our findings offer a unique platform for developing drugs against human conditions with abnormal tubulin tyrosination levels, such as cancer, heart defects and possibly brain disorders.


    Organizational Affiliation

    Department of Biology, Southern University of Science and Technology, Shenzhen, China. huanghd@sustc.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulinyl-Tyr carboxypeptidase 2A, C257Homo sapiensMutation(s): 0 
Gene Names: VASH2VASHL
EC: 3.4.17.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q86V25 (Homo sapiens)
Explore Q86V25 
Go to UniProtKB:  Q86V25
PHAROS:  Q86V25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86V25
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small vasohibin-binding proteinB, D74Homo sapiensMutation(s): 0 
Gene Names: SVBPCCDC23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N300 (Homo sapiens)
Explore Q8N300 
Go to UniProtKB:  Q8N300
PHAROS:  Q8N300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N300
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.887α = 90
b = 119.887β = 90
c = 102.636γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.3: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.4: 2019-07-17
    Changes: Data collection, Database references