4G0A

Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5'-GG Sequence for RTPase activity

Summary for 4G0A

• Entry DOI: 10.2210/pdb4g0a/pdb
• Descriptor: Non-structural protein 2, RNA (5'-R(P*GP*GP*U)-3'), CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: rna triphosphatase, rna binding, hydrolase activity, nucleotide binding, metal ion binding, host cell cytoplasm, hydrolase-rna complex, hydrolase/rna
• Biological source: Simian 11 rotavirus (RV-A); More
• Cellular location: Host cytoplasm (Potential): Q03243
• Total number of polymer chains: 8
• Total formula weight: 150444.31

Authors

Hu, L.,Prasad, B.V.V. (deposition date: 2012-07-09, release date: 2012-08-22, Last modification date: 2024-02-28)

Primary citation

Hu, L.,Chow, D.C.,Patton, J.T.,Palzkill, T.,Estes, M.K.,Prasad, B.V.
Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5' GG Sequence for RTPase Activity.
J.Virol., 86:10547-10557, 2012

PubMed Abstract: Rotavirus nonstructural protein NSP2, a functional octamer, is critical for the formation of viroplasms, which are exclusive sites for replication and packaging of the segmented double-stranded RNA (dsRNA) rotavirus genome. As a component of replication intermediates, NSP2 is also implicated in various replication-related activities. In addition to sequence-independent single-stranded RNA-binding and helix-destabilizing activities, NSP2 exhibits monomer-associated nucleoside and 5' RNA triphosphatase (NTPase/RTPase) activities that are mediated by a conserved H225 residue within a narrow enzymatic cleft. Lack of a 5' γ-phosphate is a common feature of the negative-strand RNA [(-)RNA] of the packaged dsRNA segments in rotavirus. Strikingly, all (-)RNAs (of group A rotaviruses) have a 5' GG dinucleotide sequence. As the only rotavirus protein with 5' RTPase activity, NSP2 is implicated in the removal of the γ-phosphate from the rotavirus (-)RNA. To understand how NSP2, despite its sequence-independent RNA-binding property, recognizes (-)RNA to hydrolyze the γ-phosphate within the catalytic cleft, we determined a crystal structure of NSP2 in complex with the 5' consensus sequence of minus-strand rotavirus RNA. Our studies show that the 5' GG of the bound oligoribonucleotide interacts extensively with highly conserved residues in the NSP2 enzymatic cleft. Although these residues provide GG-specific interactions, surface plasmon resonance studies suggest that the C-terminal helix and other basic residues outside the enzymatic cleft account for sequence-independent RNA binding of NSP2. A novel observation from our studies, which may have implications in viroplasm formation, is that the C-terminal helix of NSP2 exhibits two distinct conformations and engages in domain-swapping interactions, which result in the formation of NSP2 octamer chains.

PubMed: 22811529
DOI: 10.1128/JVI.01201-12

Experimental method

X-RAY DIFFRACTION (2.0995 Å)