PROSITE documentation PDOC52111

Filoviruses viral protein 35 (VP35) nucleoprotein (NP) binding peptide (NPBP) domain profile

The Ebolavirus (EBOV) and Marburgvirus (MARV) belong to the Filoviridae family [E1], a group of filamentous, single-stranded, negative-sensed RNA viruses. Upon infection, uncontrolled propagation of EBOV and MARV causes severe hemorrhagic fevers with high mortality rates. So far, six species of EBOV have been identified, including Bundibugyo, Reston, Sudan, Tai Forest, Bombali, and Zaire Ebolavirus, while Lake Victoria Marburgvirus is the only member in MARV. The genomes of MARV and EBOV encode seven viral proteins in tandem: nucleoprotein (N), viral protein (VP35), VP40, glycoprotein (GP), VP30, VP24, and large protein (L). The viral genome is encapsidated by N proteins, forming a helical nucleocapsid (NC) that serves as template for replication and transcription. These processes are critical to the viral life cycle and are facilitated by the RNA-dependent RNA polymerase (RdRp) complex, consisting of the L protein and its essential cofactor VP35. L contains all of the enzymatic activity required for RNA transcription and replication. Filovirus VP35 is a multifunctional protein, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. The filovirus VP35 N-terminal region contains a nucleoprotein (NP) binding peptide (NPBP), which regulates NP oligomerization and ssRNA binding, followed by an oligomerization domain (OD) that bridges the interaction between NP and L polymerase important for RNA synthesis. The C-terminal interferon (IFN) inhibitory domain (IID) is largely responsible for innate immune antagonism (see <PDOC51735>).

The association of NP with VP35 has been shown to play a critical role during the encapsidation of viral RNA. The N-terminal VP35 NPBP is a 28 residues-long domain, which chaperones the N-terminal core domain of NP (NP core) in a monomeric and RNA-free form until it reaches the RNA-binding niche. VP35 thereby prevents the premature polymerization of NP in the absence of viral genomes and also prevents polymerization on cellular RNAs. At sites of viral RNA synthesis, VP35 releases NP, allowing it to polymerize with other copies of NP contained in the growing NC. Stepwise addition of NP promotes encapsidation of the viral RNA [1,2,3,4,5,6,7,8,9,10].

The NPBP domain adopts two orthogonal helices, one α-helix and a 3(10)-helix turn, that form multiple hydrogen bonds and non-bonded contacts with NP (see <PDB:4YPI>). The interactions between the NP core domain and the VP35 NPBP domain are mainly hydrophobic interactions. The VP35 NPBP domain binds a hydrophobic pocket on one side of the C-terminal lobe (foot lobe) of NP in an interface that overlaps with the NP oligomerization site and does not occlude the RNA binding site. Although there are variations in the N and C termini of the NPBP peptides between EBOV and MARV, most of the key residues for NP binding are conserved between the viruses [6,7,8,9,10].

The profile we developed covers the entire VP35 NPBP domain.