PROSITE documentation PDOC51954

Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile

Coronaviruses (CoVs) are enveloped positive-strand RNA viruses that infect many species, including humans, other mammals, and birds. After infection, the host may develop respiratory, bowel, liver, and neurological diseases. Coronaviruses are divided into four genera: αcoronavirus, βcoronavirus, γcoronavirus, and Deltacoronavirus. The ideal hosts of αCoV and βCoV are mammals, and γCoV primarily infects birds, while DeltaCoV has been identified in both mammals and birds. SARS, SARS-CoV-2, BatCoV RaTG13 and Bat-SARS-like coronavirus (BATSL-CoVZXC21 and BAT-SL-CoVZC45) belong to the Sarbecovirus subgenus of βCoV [E1].

The CoV replicase gene encodes two overlapping polyproteins, termed pp1a and pp1ab, which mediate viral replication and transcription. The polypeptides pp1a and pp1ab are processed by the action of a main protease (Nsp5) (see <PDOC51442>) and of one or two papain-like proteases (PLpro) (see <PDOC51124>) found in Nsp3 into non-structural proteins (Nsps) that predominantly play a role in replication and transcription. Within these Nsps, the bifunctional Nsp14 contains an N-terminal exoribonuclease (ExoN) domain playing a proofreading role for prevention of lethal mutagenesis (see <PDOC51953>) and a C-terminal domain that functions as an S-adenosyl methionine (SAM)-dependent guanine-N7-methyltransferase (N7-MTase) for mRNA capping. Assembly of a cap1 structure at the 5' end of viral mRNA assists in translation and evading host defense. The cap structure consists of a 7-methylguanosine (m7G) linked to the first nucleotide of the RNA transcript through a 5'-5' triphosphate bridge. Formation of this cap in CoV requires four sequential reactions. First, Nsp13 RNA triphosphatase (RTPase) hydrolyzes nascent RNA to yield pp-RNA. Then an unknown guanylyl-transferase (GTase) hydrolyzes GTP, transfers the product GMP to pp-RNA, and creates Gppp-RNA. Then Nsp14 methylates the 5' guanine of the Gppp-RNA at the N7 position, followed by methylation of the ribose of the first nucleotide at the 2'-O-position by Nsp16 [1,2,3,4,5,6].

The Nsp14 N7-MTase domain comprises a total of 12 β-strands and five α-helices and exhibits a noncanonical MTase fold with a rare β-sheet insertion and a peripheral zinc finger (see <PDB:5NFY>). The fold presents a central five-stranded β-sheet made up of four parallel strands and one antiparallel strand. The central β-sheet is sandwiched between a single α-helix and three long loops punctuated by two small helices. The central sheet is surrounded by two strands, which are perpendicular but not fully aligned with the central sheet. The N7-MTase domain ends with an α-helix, α5, a modification that stabilizes the local hydrophobic environment and is found in SAM-dependent MTases. A zinc finger (ZF) motif is located between strand β11 and helix α4 and is important for the proper folding of this region. The cap-precursor guanosine-P3-adenosine-5',5'-triphosphate (GpppA) and SAM bind in proximity in a highly constricted pocket between two β-sheets to accomplish methyl transfer. In comparison with the conventional SAM-binding motif [DEY]-x-G-x-G-x-G, the corresponding conserved motif in CoV N7-MTase is D-x-G-x-P-x-[GA]. The cap structure (GpppA) binds between two β-strands (β1 and β2) and helix 1 [1,2,3,4,5,6].

The profile we developed covers the entire CoV N7-MTase domain.