3Q1R

Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader

Replaces:  3OKB

Summary for 3Q1R

• Entry DOI: 10.2210/pdb3q1r/pdb
• Related: 1EHZ 1NBS 1NZ0 1U9S 2A2E 2A64 3Q1Q
• Descriptor: RNase P RNA, Ribonuclease P protein component, TRNA (PHE), ... (5 entities in total)
• Functional Keywords: rnase p, ribozyme, ribonuclease p, trna, pre-trna, tetraloop-receptor, ribose zipper, a-minor interaction, base stacking, intermolecular base pairs, intermolecular rna-rna contacts, rnp, ribonucleoprotein complex, enzyme-product complex, metalloenzyme, rna-metal interactions, shape complementarity, substrate recognition, endonuclease, hydrolase-rna complex, hydrolase/rna
• Biological source: Thermotoga maritima; More
• Total number of polymer chains: 4
• Total formula weight: 157026.17

Authors

Reiter, N.J.,Ostermanm, A.,Torres-Larios, A.,Swinger, K.K.,Pan, T.,Mondragon, A. (deposition date: 2010-12-17, release date: 2011-03-09, Last modification date: 2023-09-13)

Primary citation

Reiter, N.J.,Osterman, A.,Torres-Larios, A.,Swinger, K.K.,Pan, T.,Mondragon, A.
Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA.
Nature, 468:784-789, 2010

PubMed Abstract: Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5' leader sequence with and without metal help to identify the 5' substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P.

PubMed: 21076397
DOI: 10.1038/NATURE09516

Experimental method

X-RAY DIFFRACTION (4.21 Å)