3GCA
The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain
Summary for 3GCA
| Entry DOI | 10.2210/pdb3gca/pdb |
| Descriptor | PreQ1 riboswitch, 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE, SULFATE ION (3 entities in total) |
| Functional Keywords | preq1, preq0, riboswitch, rna, ribosomal binding site, amptamer, metabolite |
| Total number of polymer chains | 1 |
| Total formula weight | 10966.69 |
| Authors | Spitale, R.C.,Wedekind, J.E. (deposition date: 2009-02-21, release date: 2009-03-03, Last modification date: 2024-02-21) |
| Primary citation | Spitale, R.C.,Torelli, A.T.,Krucinska, J.,Bandarian, V.,Wedekind, J.E. The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain. J.Biol.Chem., 284:11012-11016, 2009 Cited by PubMed Abstract: Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ(1) riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ(1) aptamer domain in complex with its precursor metabolite preQ(0). The structure is highly compact with a core that features a stem capped by a well organized decaloop. The metabolite is recognized within a deep pocket via Watson-Crick pairing with C15. Additional hydrogen bonds are made to invariant bases U6 and A29. The ligand-bound state confers continuous helical stacking throughout the core fold, thus providing a platform to promote Watson-Crick base pairing between C9 of the decaloop and the first base of the ribosome-binding site, G33. The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated. PubMed: 19261617DOI: 10.1074/jbc.C900024200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.75 Å) |
Structure validation
Download full validation report
