2r7u
From Proteopedia
Crystal Structure of Rotavirus SA11 VP1/RNA (AAAAGCC) Complex
Structural highlights
Function[RDRP_ROTSP] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedRotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 A resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus lambda3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication. Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.,Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC Structure. 2008 Nov 12;16(11):1678-88. PMID:19000820[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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