3Q1Q: Structure Of A Bacterial Ribonuclease P Holoenzyme In Complex With Trna

Citation:
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.
PDB ID: 3Q1QDownload
MMDB ID: 89093
PDB Deposition Date: 2010/12/17
Updated in MMDB: 2011/05
Experimental Method:
x-ray diffraction
Resolution: 3.8  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3Q1Q: trimeric; determined by author and by software (PISA)
Molecular Components in 3Q1Q
Label Count Molecule
Protein (1 molecule)
1
Ribonuclease P Protein Component(Gene symbol: TM1463)
Molecule annotation
Nucleotides(2 molecules)
1
Rnase P RNA
Molecule annotation
1
tRNA (Phe)
Molecule annotation
Chemicals (6 molecules)
1
4
2
2
* Click molecule labels to explore molecular sequence information.

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