Atlas of coronavirus replicase structure

Abstract

The international response to SARS-CoV has produced an outstanding number of protein structures in a very short time. This review summarizes the findings of functional and structural studies including those derived from cryoelectron microscopy, small angle X-ray scattering, NMR spectroscopy, and X-ray crystallography, and incorporates bioinformatics predictions where no structural data is available. Structures that shed light on the function and biological roles of the proteins in viral replication and pathogenesis are highlighted. The high percentage of novel protein folds identified among SARS-CoV proteins is discussed.

Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles

“…It appears that domains from PL2 pro to the CoVeY domain have not undergone significant deletion or rearrangement during coronavirus evolution, while other nsps like nsp1, nsp2, and the Nterminal regions of nsp3 clearly have evolved by duplication and deletion of domains (Neuman et al, 2008(Neuman et al, , 2014b. The C-terminal portion of nsp3 has been shown to change the localization of nsp4 (Hagemeijer et al, 2011), and cause a membrane proliferation phenotype in transfected cells (Angelini et al, 2013).…”

The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing

“…A multitude of enzymatic functions has been identified and characterized in vitro, although mainly using artificial substrates so far. Protein structures were obtained for most of the subunits from the nsp7-16 region (Neuman et al, 2014b), but unfortunately two prominent remaining "blank spots" on this map concern two key enzymes in CoV RNA synthesis, RdRp and helicase. Filling those gaps would constitute an important step forward, to address basic questions like the priming mechanism employed by the RdRp and the function of the NiRAN domain, and to accelerate targeted drug discovery, for example, in the area of nucleoside inhibitors of CoV RNA synthesis, which has received little attention thus far.…”

“…1) that are working together during CoV replication (Ziebuhr et al, 2000). Second, using this information and promoted by rapidly advancing methods in structural biology, X-ray or NMR structures were obtained for numerous (recombinant) full-length CoV nsps or domains thereof, in particular for SARS-CoV (Neuman et al, 2014b). Third, multiple techniques for the targeted mutagenesis of CoV genomes were developed and refined, which was a specific technical challenge due to the exceptionally large size of the CoV RNA genome (Almazan et al, 2014).…”

MERS coronavirus outbreak: Implications for emerging viral infections

“…Individual nsp proteins have different roles in viral replication. For example, nsp3 has a papain-like protease (PLpro) activity which mediates the initial processing of pp1a (Forni et al, 2016;Hagemeijer et al, 2012;Neuman et al, 2014). Nsp3 also works with nsp4 and nsp6 to anchor the viral RTC to intracellular membranes and form a reticulovesicular membranous network where the viral RNA can replicate.…”