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Unique SARS

PSI-SGKB [doi:10.1038/fa_psisgkb.2009.12]
Featured Article - April 2009
Short description: The solution structure of the SARS unique domain confirms that it binds single-stranded RNA and hints at its function.J. Virol. 83, 1823-1836 (2009)

Severe acute respiratory syndrome (SARS) is a highly contagious human disease caused by the SARS-associated coronavirus (SARS-CoV). A pandemic in 2003 resulted in nearly 800 deaths and spread round the world in just a few weeks. The virus was controlled by public-health measures, but the search for effective drugs and a vaccine continues.

The structure determination of the central segment of the SARS-unique domain (SUD-M) closes an important gap in the structural coverage of the N-terminal half of the 1922-residue nonstructural protein 3 of the SARS coronavirus (upper panel). Two views of the NMR structure of SUD-M are shown in the dotted box. In the space-filling model, the surface area that was affected by poly(A) single-stranded RNA binding is highlighted in magenta, indicating possible locations for the active site. (PDB

SARS-CoV has an RNA genome of 29.7 kb, which is thought to encode 16 non-structural proteins (nsp1 to nsp16), plus structural and accessory proteins. The non-structural proteins are particularly interesting because they form a membrane-associated complex that carries out the replication and processing of the viral RNA genome. A previous study exploring the cellular events during early viral infection highlighted the importance of nsp3.

Nsp3 is a large (1,922 residues) multidomain protein. Three of its domains have previously been characterized: nsp3a (residues 1–183) has a ubiquitin fold and binds RNA; nsp3b (184–351) is a poly(ADP-ribose)-binding protein and has ADP-ribose-1″-phosphatase activity; and nsp3d (723–1037) contains a ubiquitin-related fold and a papain-like protease. It also contains other, little-studied, functional domains, of which nsp3c is of special interest because it seems to be unique to SARS-CoV and is known as the 'SARS-unique domain' (SUD).

Chatterjee et al., part of PSI JCSG, have solved the NMR structure of a globular domain called SUD-M, which occupies the central part of the SUD region. SUD-M consists of a macrodomain fold, with six β-strands forming the protein core and α-helices forming the outer layer, and it is flanked by two flexibly extended polypeptide segments.

Despite a very low sequence identity of only 5%, SUD-M and nsp3b have very similar three-dimensional structural homology and one perhaps arose from a duplication process. Structural comparison reveals a potential substrate-binding cleft within SUD-M, but the differing surface topologies suggest that the two proteins do not have the same substrate. SUD-M also has homology to several helicases, but lacks the characteristic helicase sequence. So the question is what does SUD-M bind?

Following up on their previous work, and other observations, Chatterjee et al. assessed the binding of the possible substrates single-stranded polyadenosine (poly(A)) and nucleoside triphosphate (NTP) to SUD-M using NMR chemical shift perturbation techniques. Their experiments reveal that SUD-M binds single-stranded RNA but not NTPs, and their investigations identify RNA contacts on the protein surface. Electrophoretic mobility shift assays confirm this finding, and show that purine bases have higher affinity for SUD-M than do pyrimidines.

The exact function of SUD-M remains elusive, but the additional confirmation of poly(A) single-stranded RNA binding and its structure hint that SUD-M is involved in a transcription initiation step in coronavirus replication. This now forms a platform for further experiments to clarify the role of SUD-M.

Maria Hodges

References

  1. A. Chatterjee et al. Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.
    J. Virol. 83, 1823-1836 (2009).

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