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Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

Chatterjee, A., Johnson, M. A., Serrano, P., Pedrini, B., Joseph, J. S., Neuman, B. W., Saikatendu, K., Buchmeier, M. J., Kuhn, P. and Wüthrich, K. (2009) Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. Journal of Virology, 83 (4). pp. 1823-1836. ISSN 0022-538X

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To link to this article DOI: 10.1128/jvi.01781-08

Abstract/Summary

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences > School of Biological Sciences
ID Code:9583
Uncontrolled Keywords:Electrophoretic Mobility Shift Assay; *Magnetic Resonance Spectroscopy; Models, Molecular Protein Binding; Protein Structure, Tertiary RNA/metabolism RNA Replicase/*chemistry RNA-Binding Proteins/chemistry SARS Virus/*chemistry Viral Nonstructural Proteins/*chemistry NMR STRUCTURE DETERMINATION, TORSION ANGLE DYNAMICS, SARS-CORONAVIRUS, NONSTRUCTURAL PROTEIN-3, CHEMICAL-SHIFTS, NOESY SPECTRA, ASSIGNMENT, SEQUENCE, PROGRAM, BINDING
Additional Information:Chatterjee, Amarnath Johnson, Margaret A Serrano, Pedro Pedrini, Bill Joseph, Jeremiah S Neuman, Benjamin W Saikatendu, Kumar Buchmeier, Michael J Kuhn, Peter Wuthrich, Kurt HHSN266200400058C/PHS HHS/United States U54-GM074898/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't United States Journal of virology J Virol. 2009 Feb;83(4):1823-36. Epub 2008 Dec 3.

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