3CTK

Crystal structure of the type 1 RIP bouganin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure/function studies on two type 1 ribosome inactivating proteins: Bouganin and lychnin.

Fermani, S.Tosi, G.Farini, V.Polito, L.Falini, G.Ripamonti, A.Barbieri, L.Chambery, A.Bolognesi, A.

(2009) J Struct Biol 168: 278-287

  • DOI: https://doi.org/10.1016/j.jsb.2009.07.010
  • Primary Citation of Related Structures:  
    3CTK

  • PubMed Abstract: 

    The three-dimensional structures of two type 1 RIPs, bouganin and lychnin, has been solved. Their adenine polynucleotide glycosylase activity was also determined together with other known RIPs: dianthin 30, PAP-R, momordin I, ricin A chain and saporin-S6. Saporin-S6 releases the highest number of adenine molecules from rat ribosomes, and poly(A), while its efficiency is similar to dianthin 30, bouganin and PAP-R on herring sperm DNA. Measures of the protein synthesis inhibitory activity confirmed that saporin-S6 is the most active. The overall structure of bouganin and lychnin is similar to the other considered RIPs and the typical RIP fold is conserved. The superimpositioning of their C(alpha) atoms highlights some differences in the N-terminal and C-terminal domains. A detailed structural analysis indicates that the efficiency of saporin-S6 on various polynucleotides can be ascribed to a negative electrostatic surface potential at the active site and several exposed positively charged residues in the region around that site. These two conditions, not present at the same time in other examined RIPs, could guarantee an efficient interaction with the substrate and an efficient catalysis.


  • Organizational Affiliation

    Department of Chemistry "G. Ciamician", Alma Mater Studiorum University of Bologna, Italy. simona.fermani@unibo.it


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA N-glycosidase248Bougainvillea spectabilisMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for Q8W4U4 (Bougainvillea spectabilis)
Explore Q8W4U4 
Go to UniProtKB:  Q8W4U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8W4U4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.838α = 90
b = 77.501β = 90
c = 79.383γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Database references