PDBsum entry 1w4c

Hydrolase

PDB id: 1w4c

Contents

Protein chains

(+ 1 more) 289 a.a.

(+ 11 more) 304 a.a.

Waters ×3162

References listed in PDB file

Key reference

Title

Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation.

Authors

E.J.Mancini, D.E.Kainov, J.M.Grimes, R.Tuma, D.H.Bamford, D.I.Stuart.

Ref.

Cell, 2004, 118, 743-755. [DOI no: 10.1016/j.cell.2004.09.007]

PubMed id

15369673

Abstract

Many viruses package their genome into preformed capsids using packaging motors powered by the hydrolysis of ATP. The hexameric ATPase P4 of dsRNA bacteriophage phi12, located at the vertices of the icosahedral capsid, is such a packaging motor. We have captured crystallographic structures of P4 for all the key points along the catalytic pathway, including apo, substrate analog bound, and product bound. Substrate and product binding have been observed as both binary complexes and ternary complexes with divalent cations. These structures reveal large movements of the putative RNA binding loop, which are coupled with nucleotide binding and hydrolysis, indicating how ATP hydrolysis drives RNA translocation through cooperative conformational changes. Two distinct conformations of bound nucleotide triphosphate suggest how hydrolysis is activated by RNA binding. This provides a model for chemomechanical coupling for a prototype of the large family of hexameric helicases and oligonucleotide translocating enzymes.

Figure 2.
Figure 2. Structure of the P4 Hexamer(A) The P4 hexamer is shown in terms of its secondary structural elements and solvent accessible surface in top, side, and bottom views. The secondary structural elements are colored according to the bar where different colors distinguish subdomains or segments of the P4 monomer: N-terminal safety pin motif (blue), all β domain (dark purple), conserved RecA-like ATP binding domain (red), and antiparallel β strands and C-terminal helix (green). Six molecules of AMPcPP, drawn as ball-and-stick representations, are located in clefts between monomers. The solvent-accessible surface of P4 (without nucleotides) is colored according to the electrostatic potential (defined in the key). The top view shows the solvent-exposed face of the P4 hexamer, while the bottom view shows the C-terminal face that packs against the procapsid. Representations and calculations were performed with GRASP (Nicholls et al., 1991).(B) Cartoon showing the position of the P4 hexamer (red) on the empty φ12 procapsid (green) while packaging ssRNA (cyan).

Figure 3.
Figure 3. The Nucleotide Binding SiteResidues involved in nucleotide binding and catalysis and elements of secondary structure in the cleft between two P4 monomers (cyan and purple). Nucleotides and selected residues of the active site are drawn in a ball-and-stick representation. Residues are labeled in black only in the first panel. The nucleotides are color coded according to their conformation: AMPcPP inactive “I” (orange), AMPcPP active “A” (red), product “P” (blue), and ADP-Mg^2+ (yellow). The electron density for the bound nucleotides and ions, calculated from the final Fourier difference (2F[o] − F[c]), is shown in a beige surface representation (1.0 σ). Mg^2+ ions are shown as pink balls, while the anomalous Fourier difference map for the Mn^2+ ions is shown as magenta chicken wire. The phosphates are anchored by residues of the P loop (colored in red). The views are chosen to be equivalent for each nucleotide binding site. The associated cartoon representation shows the coordination of nucleotides to selected residues of the catalytic sites and divalent cations. Distances (in Å) are shown as dotted lines.

The above figures are reprinted by permission from Cell Press: Cell (2004, 118, 743-755) copyright 2004.