|3iwn, resolution 3.20Å ()|
|Gene:||SNRPA, U1A (Homo sapiens)|
Co-crystal structure of a bacterial c-di-GMP riboswitch
The cyclic diguanylate (bis-(3'-5')-cyclic dimeric guanosine monophosphate, c-di-GMP) riboswitch is the first known example of a gene-regulatory RNA that binds a second messenger. c-di-GMP is widely used by bacteria to regulate processes ranging from biofilm formation to the expression of virulence genes. The cocrystal structure of the c-di-GMP responsive GEMM riboswitch upstream of the tfoX gene of Vibrio cholerae reveals the second messenger binding the RNA at a three-helix junction. The two-fold symmetric second messenger is recognized asymmetrically by the monomeric riboswitch using canonical and noncanonical base-pairing as well as intercalation. These interactions explain how the RNA discriminates against cyclic diadenylate (c-di-AMP), a putative bacterial second messenger. Small-angle X-ray scattering and biochemical analyses indicate that the RNA undergoes compaction and large-scale structural rearrangement in response to ligand binding, consistent with organization of the core three-helix junction of the riboswitch concomitant with binding of c-di-GMP.
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch., Kulshina N, Baird NJ, Ferre-D'Amare AR, Nat Struct Mol Biol. 2009 Dec;16(12):1212-7. Epub 2009 Nov 8. PMID:19898478
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
3iwn is a 4 chain structure with sequence from Homo sapiens. The October 2010 RCSB PDB Molecule of the Month feature on Riboswitches by David Goodsell is 10.2210/rcsb_pdb/mom_2010_10. Full crystallographic information is available from OCA.