1M5K

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

Replaces:  1HP6

Summary for 1M5K

• Entry DOI: 10.2210/pdb1m5k/pdb
• Related: 1M5K 1M5O 1M5P 1M5V
• Descriptor: RNA INHIBITOR SUBSTRATE, RNA HAIRPIN RIBOZYME, PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A), ... (6 entities in total)
• Functional Keywords: hairpin ribozyme, catalytic rna, u1a rna binding protein docked conformation, substrate inhibitor strand, translation-rna complex, translation/rna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 6
• Total formula weight: 97809.71

Authors

Rupert, P.B.,Ferre-D'Amare, A.R. (deposition date: 2002-07-09, release date: 2002-08-02, Last modification date: 2024-02-14)

Primary citation

Rupert, P.B.,Massey, A.P.,Sigurdsson, S.T.,Ferre-D'Amare, A.R.
Transition state stabilization by a catalytic RNA
Science, 298:1421-1424, 2002

PubMed Abstract: The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.

PubMed: 11298439
DOI: 10.1126/science.1076093

Experimental method

X-RAY DIFFRACTION (2.4 Å)