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Structure paper

TitleStructural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
Journal, issue, pagesMol Cell, Vol. 83, Issue 21, Page 3921-33930.e7, Year 2023
Publish dateNov 2, 2023
AuthorsGabriel I Small / Olga Fedorova / Paul Dominic B Olinares / Joshua Chandanani / Anoosha Banerjee / Young Joo Choi / Henrik Molina / Brian T Chait / Seth A Darst / Elizabeth A Campbell /
PubMed AbstractThe enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with ...The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
External linksMol Cell / PubMed:37890482 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.06 Å
Structure data

40699

8sq9

EMDB-40699, PDB-8sq9:
SARS-CoV-2 replication-transcription complex bound to nsp9 and UMPCPP, as a pre-catalytic NMPylation intermediate
Method: EM (single particle) / Resolution: 2.9 Å

40707

8sqj

EMDB-40707, PDB-8sqj:
SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, as a noncatalytic RNA-nsp9 binding mode
Method: EM (single particle) / Resolution: 3.06 Å

40708

8sqk

EMDB-40708, PDB-8sqk:
SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate
Method: EM (single particle) / Resolution: 3.01 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-WSB:
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine

ChemComp-HOH:
WATER / Water

ChemComp-VSN:
5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine

Source
  • severe acute respiratory syndrome coronavirus 2
  • severe acute respiratory syndrome coronavirus
KeywordsVIRAL PROTEIN / RTC / nsp12 / nsp9 / NiRAN / SARS-CoV-2 / NMPylation / UMPCPP / deRNAylation / mRNA capping

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