3HAX

Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus

Summary for 3HAX

• Entry DOI: 10.2210/pdb3hax/pdb
• Related: 3HAY
• Descriptor: Probable tRNA pseudouridine synthase B, MAGNESIUM ION, Ribosome biogenesis protein Nop10, ... (11 entities in total)
• Functional Keywords: h/aca, guide rna, rna-protein complex, pseudouridine synthase, isomerase, trna processing, ribonucleoprotein, ribosome biogenesis, rrna processing, ribosomal protein, rna-binding, isomerase-biosynthetic protein-rna complex, isomerase/biosynthetic protein/rna
• Biological source: Pyrococcus furiosus; More
• Total number of polymer chains: 5
• Total formula weight: 86627.59

Authors

Ye, K. (deposition date: 2009-05-03, release date: 2009-06-23, Last modification date: 2023-11-01)

Primary citation

Duan, J.,Li, L.,Lu, J.,Wang, W.,Ye, K.
Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.
Mol.Cell, 34:427-439, 2009

PubMed Abstract: H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.

PubMed: 19481523
DOI: 10.1016/j.molcel.2009.05.005

Experimental method

X-RAY DIFFRACTION (2.11 Å)