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5O62

The structure of the thermobifida fusca guanidine III riboswitch with 1-Ethylguanidine.

Summary for 5O62
Entry DOI10.2210/pdb5o62/pdb
DescriptorRNA (41-MER), N-ETHYLGUANIDINE, MAGNESIUM ION, ... (4 entities in total)
Functional Keywordsguanidine iii riboswitch, stem-loop, pseudoknot, rna, gene regulation
Biological sourceThermobifida fusca
Total number of polymer chains2
Total formula weight27033.05
Authors
Huang, L.,Wang, J.,Lilley, D.M.J. (deposition date: 2017-06-04, release date: 2017-10-18, Last modification date: 2024-05-08)
Primary citationHuang, L.,Wang, J.,Wilson, T.J.,Lilley, D.M.J.
Structure of the Guanidine III Riboswitch.
Cell Chem Biol, 24:1407-1415.e2, 2017
Cited by
PubMed Abstract: Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site. The ligand is hydrogen bonded to the Hoogsteen edges of two guanine bases. The binding pocket has a side opening that can accommodate a small side chain, shown by structures with bound methylguanidine, aminoguanidine, ethylguanidine, and agmatine. Comparison of the new structure with those of the guanidine I and II riboswitches reveals that evolution generated three different structural solutions for guanidine binding and subsequent gene regulation, although with some common elements.
PubMed: 28988949
DOI: 10.1016/j.chembiol.2017.08.021
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.119 Å)
Structure validation

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