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NMR Structure of Small Protein B (SmpB) from Aquifex aeolicusNMR Structure of Small Protein B (SmpB) from Aquifex aeolicus
Structural highlights
FunctionSSRP_AQUAE Binds specifically to the SsrA RNA (tmRNA) and is required for stable association of SsrA with ribosomes. 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 PubMedSmall protein B (SmpB) is an essential component of the highly conserved tmRNA-SmpB system that has the dual function of releasing stalled ribosomes from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Nuclear magnetic resonance (NMR) analysis of SmpB from Aquifex aeolicus revealed an antiparallel beta-barrel structure, with three helices packed outside the core of the barrel. While the overall structure of SmpB appears to be unique, the structure does contain an embedded oligonucleotide binding fold; in this respect SmpB has similarity to several other RNA-binding proteins that are known to be associated with translation, including IF1, ribosomal protein S17 and the N-terminal domain of aspartyl tRNA synthetase. Conserved amino acids on the protein surface that are most likely to directly interact with the tmRNA were identified. The presence of widely separated clusters of conserved amino acids suggests that SmpB could function either by stabilizing two distal regions of the tmRNA, or by facilitating an interaction between the tmRNA and another component of the translational apparatus. Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue.,Dong G, Nowakowski J, Hoffman DW EMBO J. 2002 Apr 2;21(7):1845-54. PMID:11927568[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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