1RL0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 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

  • 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: 
    • 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
    • Ribosome-inactivating proteins from plants
      Barbieri, L.,Battelli, M.G.,Stirpe, F.
      (1993) Biochim.Biophys.Acta 1154: 237
    • 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.,Sect.D 59: 1227


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antiviral protein DAP-30
A
255Dianthus caryophyllusMutation(s): 0 
EC: 3.2.2.22
Find proteins for P24476 (Dianthus caryophyllus)
Go to UniProtKB:  P24476
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.568α = 90.00
b = 78.654β = 105.39
c = 43.136γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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