2P6W

Crystal structure of a glycosyltransferase involved in the glycosylation of the major capsid of PBCV-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and function of a chlorella virus-encoded glycosyltransferase.

Zhang, Y.Xiang, Y.Van Etten, J.L.Rossmann, M.G.

(2007) Structure 15: 1031-1039

  • DOI: https://doi.org/10.1016/j.str.2007.07.006
  • Primary Citation of Related Structures:  
    2P6W, 2P72, 2P73

  • PubMed Abstract: 

    Paramecium bursaria chlorella virus-1 encodes at least five putative glycosyltransferases that are probably involved in the synthesis of the glycan components of the viral major capsid protein. The 1.6 A crystal structure of one of these glycosyltransferases (A64R) has a mixed alpha/beta fold containing a central, six-stranded beta sheet flanked by alpha helices. Crystal structures of A64R, complexed with UDP, CMP, or GDP, established that only UDP bound to A64R in the presence of Mn(2+), consistent with its high structural similarity to glycosyltransferases which utilize UDP as the sugar carrier. The structure of the complex of A64R, UDP-glucose, and Mn(2+) showed that the largest conformational change occurred when hydrogen bonds were formed with the ligands. Unlike UDP-glucose, UDP-galactose and UDP-GlcNAc did not bind to A64R, suggesting a selective binding of UDP-glucose. Thus, UDP-glucose is most likely the sugar donor for A64R, consistent with glucose occurring in the virus major capsid protein glycans.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein213Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A64R
UniProt
Find proteins for Q89399 (Paramecium bursaria Chlorella virus 1)
Explore Q89399 
Go to UniProtKB:  Q89399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89399
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.229α = 90
b = 63.017β = 115.42
c = 44.772γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations