Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein

I. Jung Chen, Jeu Ming P. Yuann, Yu Ming Chang, Shing Yen Lin, Jincun Zhao, Stanley Perlman, Yo Yu Shen, Tai Huang Huang, Ming Hon Hou

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0 Å. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.

Original languageEnglish
Pages (from-to)1054-1062
Number of pages9
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1834
Issue number6
DOIs
Publication statusPublished - 2013 Jun 1

Fingerprint

Human Coronavirus OC43
lissamine rhodamine B
Nucleocapsid Proteins
Crystal structure
RNA
Proteins
Viral RNA
Common Cold
Coronavirus
Ribonucleoproteins
Viral Genome
Site-Directed Mutagenesis
Virion
RNA-Binding Motifs
Coronavirus nucleocapsid protein
Carrier Proteins
Plasmids
Nucleocapsid
Mutagenesis
Viruses

Keywords

  • Arginine106
  • Coronaviruses
  • Nucleocapsid protein
  • RNA-binding
  • Virus replication
  • X-ray crystallography

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein. / Chen, I. Jung; Yuann, Jeu Ming P.; Chang, Yu Ming; Lin, Shing Yen; Zhao, Jincun; Perlman, Stanley; Shen, Yo Yu; Huang, Tai Huang; Hou, Ming Hon.

In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1834, No. 6, 01.06.2013, p. 1054-1062.

Research output: Contribution to journalArticle

Chen, I. Jung ; Yuann, Jeu Ming P. ; Chang, Yu Ming ; Lin, Shing Yen ; Zhao, Jincun ; Perlman, Stanley ; Shen, Yo Yu ; Huang, Tai Huang ; Hou, Ming Hon. / Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein. In: Biochimica et Biophysica Acta - Proteins and Proteomics. 2013 ; Vol. 1834, No. 6. pp. 1054-1062.
@article{1de26d13c4354ed5a9f893d2610334e0,
title = "Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein",
abstract = "Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0 {\AA}. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.",
keywords = "Arginine106, Coronaviruses, Nucleocapsid protein, RNA-binding, Virus replication, X-ray crystallography",
author = "Chen, {I. Jung} and Yuann, {Jeu Ming P.} and Chang, {Yu Ming} and Lin, {Shing Yen} and Jincun Zhao and Stanley Perlman and Shen, {Yo Yu} and Huang, {Tai Huang} and Hou, {Ming Hon}",
year = "2013",
month = "6",
day = "1",
doi = "10.1016/j.bbapap.2013.03.003",
language = "English",
volume = "1834",
pages = "1054--1062",
journal = "Biochimica et Biophysica Acta - Proteins and Proteomics",
issn = "1570-9639",
publisher = "Elsevier",
number = "6",

}

TY - JOUR

T1 - Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein

AU - Chen, I. Jung

AU - Yuann, Jeu Ming P.

AU - Chang, Yu Ming

AU - Lin, Shing Yen

AU - Zhao, Jincun

AU - Perlman, Stanley

AU - Shen, Yo Yu

AU - Huang, Tai Huang

AU - Hou, Ming Hon

PY - 2013/6/1

Y1 - 2013/6/1

N2 - Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0 Å. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.

AB - Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0 Å. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.

KW - Arginine106

KW - Coronaviruses

KW - Nucleocapsid protein

KW - RNA-binding

KW - Virus replication

KW - X-ray crystallography

UR - http://www.scopus.com/inward/record.url?scp=84878105608&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84878105608&partnerID=8YFLogxK

U2 - 10.1016/j.bbapap.2013.03.003

DO - 10.1016/j.bbapap.2013.03.003

M3 - Article

C2 - 23501675

AN - SCOPUS:84878105608

VL - 1834

SP - 1054

EP - 1062

JO - Biochimica et Biophysica Acta - Proteins and Proteomics

JF - Biochimica et Biophysica Acta - Proteins and Proteomics

SN - 1570-9639

IS - 6

ER -