Protein Name

RNA packing motor protain


Pseudomonas phage PHI12

Biological Context

It is of crucial importance for viruses to package their genome into empty capsids and thus guard it from hostile environment. The process of packaging is accomplished by very powerful 'motor proteins' that use the energy obtained from hydrolysis of the ubiquitous cell fuel ATP to transport RNA through the capsid shell. The portal protein P4 of dsRNA bacteriophage phi12 is one of the simplest nucleic acid transporters.

Structure Description


It's structure is shown here. Let's have a look at how ATP hydrolysis leads to RNA translocation. Each monomer of the hexameric P4 has a triangular shape, and can be roughly divided into three regions - a C-terminal domain, a central core and an N-terminal domain. The first two regions comprise the nucleotide-binding domain, whose structure is very similar to this domain in other hexameric ATPases (enzymes that hydrolyze ATP). It contains an eight-stranded beta-sheet and five alpha-helices enclosing it. The C-terminal domain contains hydrophobic residues that are required for binding to the virus capsid, but not needed for hexamerization. The hexamer itself has the shape of a rather thick donut. Its bottom (the side which attaches to the capsid) is formed predominantly by the C-terminal domains of the monomers, while the N-terminal ones construct the top. The size of the channel going through the middle of the P4 'donut' is the perfect one for the accommodation of a single strand of RNA, 11 bases per turn. The nucleic acid binds to helix alpha-6 (residues 239-252) and loop L2 (residues 232-239). The ATP binding pockets lie on the outer surface of the hexamer. Residues Lys136, Thr137, Glu160, and Asp189 are known to be important for the ATP driven activation process. The first two residues, Lys136 and Thr137, interact with two of the ATP phosphate groups; Glu160 activates a water molecule needed for a nucleophilic attack on the third ATP; and finally, Asp189 coordinates magnesium ions. When RNA enters the channel, one of its bases binds to loop L2 and helix alpha-6 of one of the monomers. Binding of ATP to the protein on the opposite outer side ensures that L2 and alpha-6 are firmly secured in up configuration. Hydrolysis of ATP leads to a rotation of loop P (residues 131-135). During this rotation it presses against the L2 loop. To release this tension L2 loop moves downwards along with helix alpha-6 and the bound RNA. In that manner sequential binding, hydrolysis and release of ATP create a machinery for RNA intake. On average 6 ATP molecules are needed for the transportation of 11 RNA bases. This machinery is another example of nature's efficient transformation of chemical energy - i.e. ATP hydrolysis, into mechanical work - RNA transport

Protein Data Bank (PDB)



Mancini, E.J. Kainov, D.E. Grimes, J.M. Tuma, R. Bamford, D.H. Stuart, D.I.; "Atomic Snapshots of an RNA Packaging Motor Reveal Conformational Changes Linking ATP Hydrolysis to RNA Translocation"; Cell; (2004) 118:743-755 PubMed:15369673.



author: Rossen Apostolov

Japanese version:PDB:1W44