PROSITE documentation PDOC51953

Nidovirus 3'-5' exoribonuclease (ExoN) domain profile

The largest RNA virus genomes currently known are found in the order Nidovirales, an order of positive-stranded RNA (+RNA) viruses, which includes the family Coronaviridae and also the planarian secretory cell nidovirus (PSCNV), which has the largest RNA genome identified thus far. These agents can infect a striking variety of vertebrate and invertebrate hosts, including mammals, birds, amphibians, fish, reptiles, arthropods, molluscs, and helminths. Nidoviruses employ a complex RNA-synthesizing machinery comprising a variety of non-structural proteins (Nsps). One of the postulated drivers of the expansion of nidovirus genomes is the presence of a proofreading 3'-5' exoribonuclease (ExoN) belonging to the DEDDh family, which also includes the proofreading domains of many DNA polymerases as well as other eukaryotic and prokaryotic exonucleases. ExoN may enhance the fidelity of RNA synthesis by correcting nucleotide incorporation errors made by the RNA-dependent RNA polymerase (see <PDOC50507> and <PDOC51948>). Among nidoviruses, 3'-5' ExoN activity is found in all large genome nidoviruses (coronaviruses (CoVs), toroviruses. and roniviruses), as well as in mesoniviruses. Short genome nidoviruses (arteriviruses) lack such ExoN acivity. Acquisition of such ExoN activity might have allowed nidoviruses to evolve larger genomes. In CoVs, ExoN resides in a bifunctional replicase subunit (Nsp14) whose C-terminal has (N7-guanine)-methyltransferase (N7-MTase) activity. Nsp14 is a modular protein composed of the two functional domains, bordered on their N terminus by two other structural domains. These four regions are organized as follows: (i) a flexible N terminus forming the major bifunctional part of contacts with the Nsp10 ExoN/MTase coactivator domain (see <PDOC51952>), followed by (ii) the ExoN domain, (iii) a flexible hinge region formed by a loop and three strands, and (iv) the C terminus N7-MTase domain. The bifunctional ExoN/N7-MTase organisation is conserved in most nidovirus families but the N7-MTase domain is lacking in, e.g., toroviruses, bafiniviruses and several recently discovered nidoviruses [1,2,3,4].

The ExoN domain is an α/β fold constituted of six α-helices and 9 strands, organized into three distinct β-sheets (see <PDB:5NFY>). The core of the domain is formed by a central β-sheet made up of five antiparallel strands (β9, β6, β1, β2, and β3) and surrounded by five helices (α1, α2, α3, α4, and α6). Despite of a pronounced twist of the central sheet, the fold is reminiscent of that of the DEDD exonuclease superfamily. From this central domain, between the β3 and α2 spike, a β-hairpin structure containing β4 and β5 forms a second antiparallel β-sheet binding the Nsp10 ExoN/MTase coactivator domain. In the presence of Nsp10, residues of the ExoN active site are correctly positioned and form a highly active ExoN. The third antiparallel β-sheet grows out of the base of the central core domain between α4 and β9. It is made up of β8 and β7, and presents at its base a first zinc finger motif (ZF1) that contributes to the structural stability. A second zinc finger motif (ZF2), important for catalysis, is located between α5 and α6. Although the overall structure of the nidovirus ExoN domain has diverged significantly from other proteins, the architecture of the catalytic core and active sites resembles those used by DEDD-type exonuclease, suggesting a conserved mechanism for catalysis. These enzymes catalyze the excision of nucleoside monophosphates from nucleic acids in the 3'-to-5' direction, using a mechanism that depends on two divalent metal ions and a reactive water molecule. Five conserved active-site residues arranged in three canonical motifs (I, II, and III) orchestrate ExoN activity. A His categorizes the nidovirus ExoN domain as a DEDDh-type exoribonuclease [1,2,3,4].

The profile we developed covers the entire nidovirus ExoN domain.