6DHR image
Deposition Date 2018-05-21
Release Date 2019-04-17
Last Version Date 2024-10-09
Entry Detail
PDB ID:
6DHR
Keywords:
Title:
NMR Solution structure of Rivi3
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Conformers Calculated:
50
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Rivi3
Chain IDs:A
Chain Length:29
Number of Molecules:1
Biological Source:Rinorea virgata
Ligand Molecules
Primary Citation
Discovery and Characterization of Cyclotides from Rinorea Species.
J. Nat. Prod. 81 2512 2520 (2018)
PMID: 30387611 DOI: 10.1021/acs.jnatprod.8b00572

Abstact

Cyclotides are macrocyclic cystine-knotted peptides most commonly found in the Violaceae plant family. Although Rinorea is the second-largest genera within the Violaceae family, few studies have examined whether or not they contain cyclotides. To further our understanding of cyclotide diversity and evolution, we examined the cyclotide content of two Rinorea species found in Southeast Asia: R. virgata and R. bengalensis. Seven cyclotides were isolated from R. virgata (named Rivi1-7), and a known cyclotide (cT10) was found in R. bengalensis. Loops 2, 5, and 6 of Rivi1-4 contained sequences not previously seen in corresponding loops of known cyclotides, thereby expanding our understanding of the diversity of cyclotides. In addition, the sequence of loop 2 of Rivi3 and Rivi4 were identical to some related noncyclic "acyclotides" from the Poaceae plant family. As only acyclotides, but not cyclotides, have been reported in monocotyledons thus far, our findings support an evolutionary link between monocotyledon-derived ancestral cyclotide precursors and dicotyledon-derived cyclotides. Furthermore, Rivi2 and Rivi3 had comparable cytotoxic activities to the most cytotoxic cyclotide known to date: cycloviolacin O2 from Viola odorata; yet, unlike cycloviolacin O2, they did not show hemolytic activity. Therefore, these cyclotides represent novel scaffolds for use in future anticancer drug design.

Legend

Protein

Chemical

Disease

Primary Citation of related structures