4L81
Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))
Summary for 4L81
| Entry DOI | 10.2210/pdb4l81/pdb |
| Descriptor | SAM-I/IV variant riboswitch aptamer domain, S-ADENOSYLMETHIONINE, COBALT HEXAMMINE(III), ... (4 entities in total) |
| Functional Keywords | riboswitch, gene regulation, sam binding, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 33248.09 |
| Authors | Trausch, J.J.,Reyes, F.E.,Edwards, A.L.,Batey, R.T. (deposition date: 2013-06-15, release date: 2014-05-28, Last modification date: 2023-09-20) |
| Primary citation | Trausch, J.J.,Xu, Z.,Edwards, A.L.,Reyes, F.E.,Ross, P.E.,Knight, R.,Batey, R.T. Structural basis for diversity in the SAM clan of riboswitches. Proc.Natl.Acad.Sci.USA, 111:6624-6629, 2014 Cited by PubMed Abstract: In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor. PubMed: 24753586DOI: 10.1073/pnas.1312918111 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.95 Å) |
Structure validation
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