488D image
Deposition Date 2000-02-25
Release Date 2000-03-06
Last Version Date 2023-12-27
Entry Detail
PDB ID:
488D
Keywords:
Title:
CATALYTIC RNA ENZYME-PRODUCT COMPLEX
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
Resolution:
3.10 Å
R-Value Free:
0.30
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA RIBOZYME STRAND
Chain IDs:A
Chain Length:16
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE
Chain IDs:B
Chain Length:20
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CCC B C ?
Ligand Molecules
Primary Citation
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)
PMID: 10882069 DOI: 10.1016/S1097-2765(00)80423-2

Abstact

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.

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Primary Citation of related structures