PDBsum entry 3k1v

RNA

PDB id: 3k1v

Contents

DNA/RNA

Ligands

PRF

Metals

_CA ×4

Waters ×62

References listed in PDB file

Key reference

Title

Cocrystal structure of a class I preq1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase.

Authors

D.J.Klein, T.E.Edwards, A.R.Ferré-D'Amaré.

Ref.

Nat Struct Biol, 2009, 16, 343-344. [DOI no: 10.1038/nsmb.1563]

PubMed id

19234468

Abstract

Riboswitches are mRNA domains that bind metabolites and modulate gene expression in cis. We report cocrystal structures of a remarkably compact riboswitch (34 nucleotides suffice for ligand recognition) from Bacillus subtilis that is selective for the essential nucleobase preQ(1) (7-aminomethyl-7-deazaguanine). The structures reveal a previously unrecognized pseudoknot fold and suggest a conserved gene-regulatory mechanism whereby ligand binding promotes sequestration of an RNA segment that otherwise assembles into a transcriptional antiterminator.

Figure 1.
(a) Secondary structure. Thin lines denote connectivity; outlined letters denote disordered nucleotides (base-pairing symbols follow those of ref. 14). Not shown are tertiary interactions between S1 and L3. (b) Structure cartoon. Gray, yellow and red spheres depict the disordered portion of L2, Ca^2+ and water, respectively. (c) Select L3 tertiary interactions. (d) Partially hydrated Ca^2+ ions stabilize the L1 turn. a and b depict the wild-type^2 structure, and c and d depict the sequence variant^4.

Figure 2.
(a) Phylogenetically conserved^2 binding pocket. (b) In-line probing data^2 mapped onto the structure. Nucleotides with reduced scission in the presence of preQ[1] are colored blue. Crystallographically disordered C12 and U13 (red spheres) show increased scission in the presence of preQ[1] (ref. 2). (c) Gene regulation. In the absence of preQ[1], one S2 strand (pink) instead forms part of an antiterminator. PreQ[1] stabilizes S2 and allows formation of the terminator. a and b depict the sequence variant^4 and wild-type^2 structures, respectively.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 343-344) copyright 2009.