2LBS: Solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with AAGU tetraloop hairpin

dsRBDs often bind dsRNAs with some specificity, yet the basis for this is poorly understood. Rnt1p, the major RNase III in Saccharomyces cerevisiae, cleaves RNA substrates containing hairpins capped by A/uGNN tetraloops, using its dsRBD to recognize a conserved tetraloop fold. However, the identification of a Rnt1p substrate with an AAGU tetraloop raised the question of whether Rnt1p binds to this noncanonical substrate differently than to A/uGNN tetraloops. The solution structure of Rnt1p dsRBD bound to an AAGU-capped hairpin reveals that the tetraloop undergoes a structural rearrangement upon binding to Rnt1p dsRBD to adopt a backbone conformation that is essentially the same as the AGAA tetraloop, and indicates that a conserved recognition mode is used for all Rnt1p substrates. Comparison of free and RNA-bound Rnt1p dsRBD reveals that tetraloop-specific binding requires a conformational change in helix alpha1. Our findings provide a unified model of binding site selection by this dsRBD.
PDB ID: 2LBSDownload
MMDB ID: 93234
PDB Deposition Date: 2011/4/6
Updated in MMDB: 2011/09
Experimental Method:
solution nmr
Source Organism:
Saccharomyces cerevisiae
Similar Structures:
Biological Unit for 2LBS: dimeric; determined by author
Molecular Components in 2LBS
Label Count Molecule
Protein (1 molecule)
Ribonuclease 3(Gene symbol: RNT1)
Molecule annotation
Nucleotide(1 molecule)
RNA (32-mer)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB