6VMY
Structure of the B. subtilis cobalamin riboswitch
Summary for 6VMY
| Entry DOI | 10.2210/pdb6vmy/pdb |
| Descriptor | B. subtilis cobalamin riboswitch, MAGNESIUM ION, COBALT HEXAMMINE(III), ... (5 entities in total) |
| Functional Keywords | rna, riboswitch, cobalamin, gene regulation |
| Biological source | Bacillus subtilis |
| Total number of polymer chains | 1 |
| Total formula weight | 51052.62 |
| Authors | Chan, C.W.,Mondragon, A. (deposition date: 2020-01-28, release date: 2020-06-10, Last modification date: 2024-03-06) |
| Primary citation | Chan, C.W.,Mondragon, A. Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding. Nucleic Acids Res., 48:7569-7583, 2020 Cited by PubMed Abstract: Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule. PubMed: 32544228DOI: 10.1093/nar/gkaa507 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.25 Å) |
Structure validation
Download full validation report
