Carboxyl Terminus of Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein:  Self-Association Analysis and Nucleic Acid Binding Characterization†

ABSTRACT The nucleocapsid protein (N) of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genomic RNA and is crucial for viability. However, the RNA-binding mechanism is poorly understood. We have shown previously that the N protein contains two structural domains—the N-terminal domain (NTD; residues 45 to 181) and the C-terminal dimerization domain (CTD; residues 248 to 365)—flanked by long stretches of disordered regions accounting for almost half of the entire sequence. Small-angle X-ray scattering data show that the protein is in an extended conformation and that the two structural domains of the SARS-CoV N protein are far apart. Both the NTD and the CTD have been shown to bind RNA. Here we show that all disordered regions are also capable of binding to RNA. Constructs containing multiple RNA-binding regions showed Hill coefficients greater than 1, suggesting that the N protein binds to RNA cooperatively. The effect can be explained by the “coupled-allostery” model, devised to explain the allosteric effect in a multidomain regulatory system. Although the N proteins of different coronaviruses share very low sequence homology, the physicochemical features described above may be conserved across different groups of Coronaviridae. The current results underscore the important roles of multisite nucleic acid binding and intrinsic disorder in N protein function and RNP packaging.

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Nucleic acid binding properties of recombinant Zn2 HIV-1 nucleocapsid protein are modulated by COOH-terminal processing.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)31680-0 ◽

1994 ◽

Vol 269 (36) ◽

pp. 22538-22546 ◽

Cited By ~ 3

Author(s):

R. Khan ◽

D.P. Giedroc

Keyword(s):

Nucleic Acid ◽

Nucleocapsid Protein ◽

Nucleic Acid Binding ◽

Binding Properties ◽

Hiv 1

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A non-cleavable hexahistidine affinity tag at the carboxyl-terminus of the HIV-1 Pr55Gag polyprotein alters nucleic acid binding properties

Protein Expression and Purification ◽

10.1016/j.pep.2016.10.001 ◽

2017 ◽

Vol 130 ◽

pp. 137-145 ◽

Cited By ~ 9

Author(s):

Maria C. Bewley ◽

Lisa Reinhart ◽

Matthew S. Stake ◽

Shorena Nadaraia-Hoke ◽

Leslie J. Parent ◽

...

Keyword(s):

Nucleic Acid ◽

Carboxyl Terminus ◽

Nucleic Acid Binding ◽

Affinity Tag ◽

Binding Properties ◽

Hiv 1

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Dynamics of Linker Residues Modulate the Nucleic Acid Binding Properties of the HIV-1 Nucleocapsid Protein Zinc Fingers

PLoS ONE ◽

10.1371/journal.pone.0102150 ◽

2014 ◽

Vol 9 (7) ◽

pp. e102150 ◽

Cited By ~ 10

Author(s):

Loussiné Zargarian ◽

Carine Tisné ◽

Pierre Barraud ◽

Xiaoqian Xu ◽

Nelly Morellet ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleocapsid Protein ◽

Zinc Fingers ◽

Nucleic Acid Binding ◽

Binding Properties ◽

Hiv 1

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Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States

Viruses ◽

10.3390/v12101109 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1109 ◽

Cited By ~ 1

Author(s):

Assia Mouhand ◽

Marco Pasi ◽

Marjorie Catala ◽

Loussiné Zargarian ◽

Anissa Belfetmi ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Nucleocapsid Protein ◽

Nucleic Acid Binding ◽

Binding Properties ◽

Gag Polyprotein ◽

C Terminus ◽

Viral Particles ◽

Hiv 1 ◽

Unstructured Regions

HIV-1 Gag polyprotein orchestrates the assembly of viral particles. Its C-terminus consists of the nucleocapsid (NC) domain that interacts with nucleic acids, and p1 and p6, two unstructured regions, p6 containing the motifs to bind ALIX, the cellular ESCRT factor TSG101 and the viral protein Vpr. The processing of Gag by the viral protease subsequently liberates NCp15 (NC-p1-p6), NCp9 (NC-p1) and NCp7, NCp7 displaying the optimal chaperone activity of nucleic acids. This review focuses on the nucleic acid binding properties of the NC domain in the different maturation states during the HIV-1 viral cycle.

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Fluorescence and nucleic acid binding properties of the human T-cell leukemia virus-type 1 nucleocapsid protein

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology ◽

10.1016/s0167-4838(00)00181-3 ◽

2000 ◽

Vol 1481 (2) ◽

pp. 381-394 ◽

Cited By ~ 13

Author(s):

David R Morcock ◽

Bradley P Kane ◽

José R Casas-Finet

Keyword(s):

Nucleic Acid ◽

Nucleocapsid Protein ◽

Leukemia Virus ◽

Nucleic Acid Binding ◽

Cell Leukemia ◽

Binding Properties ◽

Cell Leukemia Virus Type ◽

Human T Cell ◽

T Cell Leukemia Virus

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Nuclear Magnetic Resonance Structure of the Nucleic Acid-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 3

Journal of Virology ◽

10.1128/jvi.01253-09 ◽

2009 ◽

Vol 83 (24) ◽

pp. 12998-13008 ◽

Cited By ~ 38

Author(s):

Pedro Serrano ◽

Margaret A. Johnson ◽

Amarnath Chatterjee ◽

Benjamin W. Neuman ◽

Jeremiah S. Joseph ◽

...

Keyword(s):

Nuclear Magnetic Resonance ◽

Nucleic Acid ◽

Magnetic Resonance ◽

Severe Acute Respiratory Syndrome ◽

Binding Site ◽

Nonstructural Protein ◽

Globular Domain ◽

Nucleic Acid Binding ◽

Nonstructural Protein 3 ◽

Nuclear Magnetic

ABSTRACT The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. Two antiparallel two-strand β-sheets and two 310-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.

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