{PDOC51953} {PS51953; NIV_EXON} {BEGIN} ********************************************************* * 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 and ). 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 ), 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 alpha/beta fold constituted of six alpha-helices and 9 strands, organized into three distinct beta-sheets (see ). The core of the domain is formed by a central beta-sheet made up of five antiparallel strands (beta9, beta6, beta1, beta2, and beta3) and surrounded by five helices (alpha1, alpha2, alpha3, alpha4, and alpha6). 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 beta3 and alpha2 spike, a beta-hairpin structure containing beta4 and beta5 forms a second antiparallel beta-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 beta-sheet grows out of the base of the central core domain between alpha4 and beta9. It is made up of beta8 and beta7, 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 alpha5 and alpha6. 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. -Sequences known to belong to this class detected by the profile: ALL. -Other sequence(s) detected in Swiss-Prot: NONE. -Last update: January 2021 / First entry. [ 1] Ma Y., Wu L., Shaw N., Gao Y., Wang J., Sun Y., Lou Z., Yan L., Zhang R., Rao Z. "Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex." Proc. Natl. Acad. Sci. U. S. A. 112:9436-9441(2015). PubMed=26159422; DOI=10.1073/pnas.1508686112 [ 2] Ferron F., Subissi L., Silveira De Morais A.T., Le N.T.T., Sevajol M., Gluais L., Decroly E., Vonrhein C., Bricogne G., Canard B., Imbert I. "Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA." Proc. Natl. Acad. Sci. U. S. A. 115:E162-E171(2018). PubMed=29279395; DOI=10.1073/pnas.1718806115 [ 3] Ogando N.S., Ferron F., Decroly E., Canard B., Posthuma C.C., Snijder E.J. "The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity." Front. Microbiol. 10:1813-1813(2019). PubMed=31440227; DOI=10.3389/fmicb.2019.01813 [ 4] Ogando N.S., Zevenhoven-Dobbe J.C., van der Meer Y., Bredenbeek P.J., Posthuma C.C., Snijder E.J. "The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2." J. Virol. 94:0-0(2020). PubMed=32938769; DOI=10.1128/JVI.01246-20 -------------------------------------------------------------------------------- PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html -------------------------------------------------------------------------------- {END}