488D

CATALYTIC RNA ENZYME-PRODUCT COMPLEX

Summary for 488D

• Entry DOI: 10.2210/pdb488d/pdb
• Descriptor: RNA RIBOZYME STRAND, FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE, SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE, ... (5 entities in total)
• Functional Keywords: catalytic rna, ribozyme, enzyme-product complex, crystal lattice trapping, rna
• Total number of polymer chains: 4
• Total formula weight: 22126.15

Authors

Murray, J.B.,Szoke, H.,Szoke, A.,Scott, W.G. (deposition date: 2000-02-25, release date: 2000-03-06, Last modification date: 2023-12-27)

Primary citation

Murray, J.B.,Szoke, H.,Szoke, A.,Scott, W.G.
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.
Mol.Cell, 5:279-287, 2000

PubMed Abstract: We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure. Subsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately perpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe several interactions with functional groups on these residues that have been identified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. These interactions may therefore be relevant to the hammerhead ribozyme reaction mechanism.

PubMed: 10882069
DOI: 10.1016/S1097-2765(00)80423-2

Experimental method

X-RAY DIFFRACTION (3.1 Å)