Results tagged “RNA,” from The SIBYLS Beamline

UC Berkeley researchers, James Berger and Nathan Thomsen, used the SIBYLS beamline to solve the structure of a hexameric helicase, the Rho transcription termination factor (from E. coli), bound to both ATP mimics and an RNA substrate. The results showed that Rho functions like a rotary engine: as the motor spins, it pulls RNA strands through it’s interior. The rotary firing order of the motor is biased so that the Rho protein can walk in only one direction along the RNA chain. The results were published in the Oct 30th issue of Cell, and have recently been written up as an ALS scientific highlight.


Rambo_RNA.gifCover Illustration from the September 2009 issue of RNA: Crystal structure of the lysine riboswitch bound to lysine (Protein Data Bank code: 3d0u) Image details show RNA: ribbon; lysine: space-filling representation, red; iridium hexamine ions: space-filling representation, blue.

Riboswitches are metabolite-sensitive elements found in mRNAs that control gene expression through a regulatory secondary structural switch. Along with regulation of lysine biosynthetic genes, mutations within the lysine-responsive riboswitch (L-box) play a role in the acquisition of resistance to antimicrobial lysine analogs. To understand the structural basis for lysine binding, we have determined the 2.8 angstroms resolution crystal structure of lysine bound to the Thermotoga maritima asd lysine riboswitch ligand-binding domain. The structure reveals a complex architecture scaffolding a binding pocket completely enveloping lysine. Mutations conferring antimicrobial resistance cluster around this site as well as highly conserved long range interactions, indicating that they disrupt lysine binding or proper folding of the RNA. Comparison of the free and bound forms by x-ray crystallography, small angle x-ray scattering, and chemical probing reveals almost identical structures, indicating that lysine induces only limited and local conformational changes upon binding.

Garst AD, Héroux A, Rambo RP, Batey RT. "Crystal structure of the lysine riboswitch regulatory mRNA element." J Biol Chem. 2008 Aug 15;283(33):22347-51. Epub 2008 Jul 1.
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