PDBsum entry 488d

RNA

PDB id

488d

Contents

			DNA/RNA

			Metals

					_CD ×8

References listed in PDB file

Key reference

Title

Capture and visualization of a catalytic RNA enzyme-Product complex using crystal lattice trapping and x-Ray holographic reconstruction.

Authors

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

Ref.

Mol Cell, 2000, 5, 279-287. [DOI no: 10.1016/S1097-2765(00)80423-2]

PubMed id

10882069

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.



	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.

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