P19
From Proteopedia
Plant Viral Protein p19 Suppression of RNA Silencing
BackgroundRNA silencing is a gene inactivation system in many eukaryotes that relies on tiny RNAs as the targeting molecules. One function of RNA silencing, which is also called post-transcriptional gene silencing (PTGS) or RNA interference (RNAi), is to act in surveillance against molecular parasites, such as viruses. Double-stranded RNA triggers the RNA silencing pathway and most plant viruses use a double-stranded RNA to replicate their genome. Various plant viruses have developed evasion techniques to circumvent this surveillance system. In one such evasion strategy, the plant viral protein p19 suppresses a plant's anti-viral RNA silencing response. p19 binds with high affinity to the double-stranded RNA silencing mediator, called siRNA, and this binding sequesters the siRNA, preventing its participation in later steps of RNA silencing.
ResultsThe X-ray crystal structure of includes both protein and RNA in the complex. . The . The synthetic RNA substrate mimics the 21-nt double-stranded siRNAs that occur in the double-strand RNA-induced RNAi silencing pathway.
p19 binds the siRNA as
. Each is made of five alpha-helices and a four-stranded beta sheet. forms a continuous eight-stranded beta-sheet. The continuous eight-stranded beta-sheet of of the double stranded siRNA. This is unusual because most proteins use loops and helices to bind double-stranded RNA, for example, see 1di2, 2zi0, 2hvy or 2az0. For more detais see P19 complexed with 19-bp small interfering RNA.
Most unprecedented is the method of size selection where p19 acts as a molecular caliper reading the size of the substrate. The aromatic rings of two tryptophan residues (W39 and W42) project from the 'reading' helix near the N-terminus of each of the two p19 monomers, stacking on the terminal base-pairs and symmetrically bracketing the ends of the duplex region of the siRNA. Thus the p19 'caliper' measures and specifically selects siRNA based on the size of the duplex region. The ability of p19 to efficiently accommodate binding of duplexes ranging from 19 to 21 bp could originate in structural plasticity of the distance separating the two 'reading head' helices. Each 'reading' helix is connected to the structured core of p19 by a short flexible loop and several side-chain interactions this presumably allows some flexibility in the positioning of the RNA end-capping tryptophan residues. Many other structures use aromatic rings to stack on nucleotide bases and cap strands in helices, see F204 and Y208 of 1gm5, W639 of 1msw and 1qln. ConclusionsThe X-ray crystal structure shows the size of the duplex as the major determinant of the siRNA recognized by p19 and biochemical experiments support this assessment. In contrast, the 2-nt 3' overhang seems to have little specific contact with the protein, consistent with Vargason et al. finding comparable binding affinities of p19 for a blunt-ended 19-bp RNA duplex, lacking the typical 2-nt single-stranded 3' overhang. About this Structure1rpu is a Protein complex structure of sequences from Carnation italian ringspot virus. Full crystallographic information is available from OCA. The molecular weight of p19 protein chain designated 'a' seen in the solved structure is 15.6 kDa (138 residues visible). The molecular weight of p19 protein chain designated 'b' seen in the solved structure is 15.2 kDa (135 residues visible). Total size of the p19-RNA complex seen in the structure is 52.1 kDa. Biological Carnation italian ringspot virus p19 is 172 amino acids and full-length p19 was expressed and purified to generate the crystals in this structure. Reference for the StructureSize selective recognition of siRNA by an RNA silencing suppressor., Vargason JM, Szittya G, Burgyan J, Tanaka Hall TM, Cell 2003 Dec 26;115(7):799-811. PMID:14697199 3D structures of protein p19Updated on 12-January-2018 1rpu – P19 + SiRNA – Carnation italian ringspot virus 1rpf, 4jk0, 4kq0 - TbsvP19 (mutant) + SiRNA –Tomato bushy stunt virus Related Structures and Topics
Notes and Literature References
Additional Literature and Resources
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Categories: RNA Silencing | Post-transcriptional gene silencing (PTGS) | Small Interfering RNA | Virus | Plant Virus | Double-stranded RNA (dsRNA) | SiRNA | Carnation italian ringspot virus | Burgyan, J. | Hall, T M.T. | Szittya, G. | Vargason, J M. | Protein-rna complex | Protein complex | Rna double helix | A-form helix | Rna length recognition | Rnai | Topic Page
