3irw

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3irw, resolution 2.70Å ()
Ligands: , ,
Non-Standard Residues:
Gene: SNRPA (Homo sapiens)
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Structure of a c-di-GMP riboswitch from V. cholerae

Publication Abstract from PubMed

The second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 A resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP signaling.

Structural basis of ligand binding by a c-di-GMP riboswitch., Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA, Nat Struct Mol Biol. 2009 Dec;16(12):1218-23. Epub 2009 Nov 8. PMID:19898477

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3irw is a 2 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.

See Also

Reference

  • Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol. 2009 Dec;16(12):1218-23. Epub 2009 Nov 8. PMID:19898477 doi:10.1038/nsmb.1702

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