4l8h | pdb_00004l8h
Bacteriophage Qbeta coat protein in complex with RNA operator hairpin
Structural highlights
FunctionCAPSD_BPQBE Capsid protein self-assembles to form an icosahedral capsid with a T=3 symmetry, about 26 nm in diameter, and consisting of 89 capsid proteins dimers (178 capsid proteins) (PubMed:27671640, PubMed:19913556). Involved in viral genome encapsidation through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome (PubMed:8943226, PubMed:27671640). Binding of the capsid proteins to the viral RNA induces a conformational change required for efficient T=3 shell formation (PubMed:19913556). The capsid contains also 1 copy of the A2 maturation protein (PubMed:27671640).[1] [2] [3] Acts as a translational repressor of viral replicase synthesis late in infection. This latter function is the result of capsid protein interaction with an RNA hairpin which contains the replicase ribosome-binding site.[4] Publication Abstract from PubMedThe coat proteins of single-stranded RNA bacteriophages specifically recognize and bind to a hairpin structure in their genome at the beginning of the replicase gene. The interaction serves to repress the synthesis of the replicase enzyme late in infection and contributes to the specific encapsidation of phage RNA. While this mechanism is conserved throughout the Leviviridae family, the coat protein and operator sequences from different phages show remarkable variation, serving as prime examples for the co-evolution of protein and RNA structure. To better understand the protein-RNA interactions in this virus family, we have determined the three-dimensional structure of the coat protein from bacteriophage Qbeta bound to its cognate translational operator. The RNA binding mode of Qbeta coat protein shares several features with that of the widely studied phage MS2, but only one nucleotide base in the hairpin loop makes sequence-specific contacts with the protein. Unlike in other RNA phages, the Qbeta coat protein does not utilize an adenine-recognition pocket for binding a bulged adenine base in the hairpin stem but instead uses a stacking interaction with a tyrosine side chain to accommodate the base. The extended loop between beta strands E and F of Qbeta coat protein makes contacts with the lower part of the RNA stem, explaining the greater length dependence of the RNA helix for optimal binding to the protein. Consequently, the complex structure allows the proposal of a mechanism by which the Qbeta coat protein recognizes and discriminates in favor of its cognate RNA. Crystal Structure of the Bacteriophage Qbeta Coat Protein in Complex with the RNA Operator of the Replicase Gene.,Rumnieks J, Tars K J Mol Biol. 2013 Sep 11. pii: S0022-2836(13)00561-5. doi:, 10.1016/j.jmb.2013.08.025. PMID:24035813[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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