3IWN

Co-crystal structure of a bacterial c-di-GMP riboswitch

Summary for 3IWN

• Entry DOI: 10.2210/pdb3iwn/pdb
• Descriptor: C-di-GMP riboswitch, U1 small nuclear ribonucleoprotein A, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) (3 entities in total)
• Functional Keywords: riboswitch, rna, u1a, rna-rna binding protein complex, acetylation, mrna processing, mrna splicing, nucleus, phosphoprotein, ribonucleoprotein, rna-binding, spliceosome, rna/rna binding protein
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 4
• Total formula weight: 82659.46

Authors

Kulshina, N.,Baird, N.J.,Ferre-D'Amare, A.R. (deposition date: 2009-09-02, release date: 2009-11-10, Last modification date: 2024-02-21)

Primary citation

Kulshina, N.,Baird, N.J.,Ferre-D'Amare, A.R.
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.
Nat.Struct.Mol.Biol., 16:1212-1217, 2009

PubMed Abstract: 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.

PubMed: 19898478
DOI: 10.1038/nsmb.1701

Experimental method

X-RAY DIFFRACTION (3.2 Å)