PDBsum entry 488d

RNA

PDB id: 488d

Contents

DNA/RNA

Metals

_CD ×8

PDB id:

488d

Name:

RNA

Title:

Catalytic RNA enzyme-product complex

Structure:

RNA ribozyme strand. Chain: a. Engineered: yes. Other_details: 16-mer. First RNA fragment of cleaved substrate. Chain: b. Engineered: yes. Other_details: 20-mer, 3'-end cyclic phosphate. Second RNA fragment of cleaved substrate.

Source:

Synthetic: yes. Synthetic: yes

Biol. unit:

Tetramer (from PQS)

Resolution:

3.10Å R-factor: 0.258 R-free: 0.301

Authors:

J.B.Murray,H.Szoke,A.Szoke,W.G.Scott

Key ref:

J.B.Murray et al. (2000). Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol Cell, 5, 279-287. PubMed id: 10882069 DOI: 10.1016/S1097-2765(00)80423-2

Date:

25-Feb-00 Release date: 06-Mar-00

DNA/RNA chains

G-U-G-G-U-C-U-G-A-U-G-A-G-G-C-C 16 bases

G-G-C-C-G-A-A-A-C-U-C-G-U-A-A-G-A-G-U-CCC 20 bases

A-C-C-A-C 5 bases

G-G-C-C-G-A-A-A-C-U-C-G-U-A-A-G-A-G-U-C-A-C-C-A-C 25 bases

DOI no: 10.1016/S1097-2765(00)80423-2

Mol Cell 5:279-287 (2000)

PubMed id: 10882069

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.

J.B.Murray, H.Szöke, A.Szöke, W.G.Scott.

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.

Selected figure(s)

Figure 1.
Figure 1. The Crystal Structure of the Hammerhead Ribozyme(A) shows the three-dimensional crystal structure of the hammerhead ribozyme in its initial state conformation. (B) is a schematic diagram of this structure designed to complement (A). The enzyme strand is shown in red, the substrate strand in yellow, and the cleavage site base in green. Base pairing is indicated by white lines (with broken lines indicating noncanonical single H bond contacts), and pink lines indicate base–ribose interactions.

Figure 3.
Figure 3. Stereo Image of the Cleavage ProductThe 2′,3′-cyclic phosphate terminus of the ribozyme substrate complex is shown with various distances to the two closest residues of the enzyme strand, G-5 and A-6. Not all distances represent hydrogen bonds, as discussed in the text.

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 5, 279-287) copyright 2000.

Figures were selected by an automated process.