Solution Structure of the C-Terminal Nucleoprotein–RNA Binding Domain of the Vesicular Stomatitis Virus Phosphoprotein

Abstract

Beyond common features in their genome organization and replication mechanisms, the evolutionary relationships among viruses of the Rhabdoviridae family are difficult to decipher because of the great variability in the amino acid sequence of their proteins. The phosphoprotein (P) of vesicular stomatitis virus (VSV) is an essential component of the RNA transcription and replication machinery; in particular, it contains binding sites for the RNA-dependent RNA polymerase and for the nucleoprotein. Here, we devised a new method for defining boundaries of structured domains from multiple disorder prediction algorithms, and we identified an autonomous folding C-terminal domain in VSV P (P CTD). We show that, like the C-terminal domain of rabies virus (RV) P, VSV P CTD binds to the viral nucleocapsid (nucleoprotein–RNA complex). We solved the three-dimensional structure of VSV P CTD by NMR spectroscopy and found that the topology of its polypeptide chain resembles that of RV P CTD. The common part of both proteins could be superimposed with a backbone RMSD from mean atomic coordinates of 2.6 Å. VSV P CTD has a shorter N-terminal helix (α 1) than RV P CTD; it lacks two α-helices (helices α 3 and α 6 of RV P), and the loop between strands β 1 and β 2 is longer than that in RV. Dynamical properties measured by NMR relaxation revealed the presence of fast motions (below the nanosecond timescale) in loop regions (amino acids 209–214) and slower conformational exchange in the N- and C-terminal helices. Characterization of a longer construct indicated that P CTD is preceded by a flexible linker. The results presented here support a modular organization of VSV P, with independent folded domains separated by flexible linkers, which is conserved among different genera of Rhabdoviridae and is similar to that proposed for the P proteins of the Paramyxoviridae.