1RL0

Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 1.4A structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins

Fermani, S.Falini, G.Ripamonti, A.Polito, L.Stirpe, F.Bolognesi, A.

(2005) J Struct Biol 149: 204-212

  • DOI: 10.1016/j.jsb.2004.11.007
  • Primary Citation of Related Structures:  
    1RL0

  • PubMed Abstract: 
  • Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of ...

    Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of protein synthesis. They also depurinate extensively DNA and other polynucleotides. The three-dimensional structure of dianthin 30, a type 1 (single-chain) RIP of Dianthus caryophyllus (leaves), is now described at 1.4 angstroms, a resolution never achieved before for any RIP. The fold typical of RIPs is conserved, despite some differences in the loop regions. The general structure comparison by superimposed alpha-carbon (249 atoms) and the sequence alignment by structure for dianthin 30 and saporin-S6 give a root mean square deviation of 0.625 angstroms. Despite the differences reported for the biological activities of the two RIPs, their structures fit quite well and both show a protein segment containing strands beta7, beta8, and beta9 shorter than other RIPs. However, the surface electrostatic potential in the active site region neatly distinguishes dianthin 30 from saporin-S6. The possible relationship between the charge distribution and the behavior of the proteins toward different substrates is discussed.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of two ribosomes-inactivating proteins: lychnin and dianthin 30
      Fermani, S., Falini, G., Ripamonti, A., Bolognesi, A., Polito, L., Stirpe, F.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1227
    • Ribosome-inactivating proteins from plants
      Barbieri, L., Battelli, M.G., Stirpe, F.
      (1993) Biochim Biophys Acta 1154: 237
    • Dianthins, ribosome-damaging proteins with anti-viral properties from Dianthus caryophyllus L. (carnation)
      Stirpe, F., Williams, D.G., Onyon, L.G., Legg, R.F., Stevens, W.A.
      (1981) Biochem J 195: 399

    Organizational Affiliation

    Dipartimento di Chimica G. Ciamician, Alma Mater Studiorum Universita' di Bologna, via Selmi 2, I-40126 Bologna, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antiviral protein DAP-30A255Dianthus caryophyllusMutation(s): 0 
EC: 3.2.2.22
Find proteins for P24476 (Dianthus caryophyllus)
Explore P24476 
Go to UniProtKB:  P24476
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.568α = 90
b = 78.654β = 105.39
c = 43.136γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance