1RL0

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

DOI: 10.2210/pdb1RL0/pdb

Classification: HYDROLASE, PLANT PROTEIN
Organism(s): Dianthus caryophyllus
Mutation(s): No

Deposited: 2003-11-24 Released: 2004-12-07
Deposition Author(s): Fermani, S., Falini, G., Ripamonti, A., Bolognesi, A., Polito, L., Stirpe, F.

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

PubMed: 15681236 Search on PubMed
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 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
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiviral protein DAP-30	A	255	Dianthus caryophyllus	Mutation(s): 0 EC: 3.2.2.22
Find proteins for P24476 (Dianthus caryophyllus) Explore P24476 Go to UniProtKB: P24476
Protein Feature View Expand
Reference Sequence