Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.
Identifieur interne : 001B20 ( PubMed/Corpus ); précédent : 001B19; suivant : 001B21Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.
Auteurs : Mitsuhiro Takeda ; Chung-Ke Chang ; Teppei Ikeya ; Peter Güntert ; Yuan-Hsiang Chang ; Yen-Lan Hsu ; Tai-Huang Huang ; Masatsune KainoshoSource :
- Journal of molecular biology [ 1089-8638 ] ; 2008.
English descriptors
- KwdEn :
- Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Dimerization, Humans, Models, Molecular, Molecular Sequence Data, Molecular Structure, Mutagenesis, Site-Directed, Nuclear Magnetic Resonance, Biomolecular (methods), Nucleocapsid Proteins (chemistry), Nucleocapsid Proteins (genetics), Protein Structure, Quaternary, Protein Structure, Tertiary, Ribonucleoproteins (chemistry), Ribonucleoproteins (metabolism), SARS Virus (chemistry), Severe Acute Respiratory Syndrome (virology).
- MESH :
- chemical , chemistry : Nucleocapsid Proteins, Ribonucleoproteins.
- chemical , genetics : Nucleocapsid Proteins.
- chemical , metabolism : Ribonucleoproteins.
- chemistry : SARS Virus.
- methods : Nuclear Magnetic Resonance, Biomolecular.
- virology : Severe Acute Respiratory Syndrome.
- Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Dimerization, Humans, Models, Molecular, Molecular Sequence Data, Molecular Structure, Mutagenesis, Site-Directed, Protein Structure, Quaternary, Protein Structure, Tertiary.
Abstract
The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.
DOI: 10.1016/j.jmb.2007.11.093
PubMed: 18561946
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pubmed:18561946Le document en format XML
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uniqKey="Chang Y" first="Yuan-Hsiang" last="Chang">Yuan-Hsiang Chang</name></author><author><name sortKey="Hsu, Yen Lan" sort="Hsu, Yen Lan" uniqKey="Hsu Y" first="Yen-Lan" last="Hsu">Yen-Lan Hsu</name></author><author><name sortKey="Huang, Tai Huang" sort="Huang, Tai Huang" uniqKey="Huang T" first="Tai-Huang" last="Huang">Tai-Huang Huang</name></author><author><name sortKey="Kainosho, Masatsune" sort="Kainosho, Masatsune" uniqKey="Kainosho M" first="Masatsune" last="Kainosho">Masatsune Kainosho</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18561946</idno><idno type="pmid">18561946</idno><idno type="doi">10.1016/j.jmb.2007.11.093</idno><idno type="wicri:Area/PubMed/Corpus">001B20</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001B20</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.</title><author><name sortKey="Takeda, Mitsuhiro" sort="Takeda, Mitsuhiro" uniqKey="Takeda M" first="Mitsuhiro" last="Takeda">Mitsuhiro Takeda</name><affiliation><nlm:affiliation>Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Chang, Chung Ke" sort="Chang, Chung Ke" uniqKey="Chang C" first="Chung-Ke" last="Chang">Chung-Ke Chang</name></author><author><name sortKey="Ikeya, Teppei" sort="Ikeya, Teppei" uniqKey="Ikeya T" first="Teppei" last="Ikeya">Teppei Ikeya</name></author><author><name sortKey="Guntert, Peter" sort="Guntert, Peter" uniqKey="Guntert P" first="Peter" last="Güntert">Peter Güntert</name></author><author><name sortKey="Chang, Yuan Hsiang" sort="Chang, Yuan Hsiang" uniqKey="Chang Y" first="Yuan-Hsiang" last="Chang">Yuan-Hsiang Chang</name></author><author><name sortKey="Hsu, Yen Lan" sort="Hsu, Yen Lan" uniqKey="Hsu Y" first="Yen-Lan" last="Hsu">Yen-Lan Hsu</name></author><author><name sortKey="Huang, Tai Huang" sort="Huang, Tai Huang" uniqKey="Huang T" first="Tai-Huang" last="Huang">Tai-Huang Huang</name></author><author><name sortKey="Kainosho, Masatsune" sort="Kainosho, Masatsune" uniqKey="Kainosho M" first="Masatsune" last="Kainosho">Masatsune Kainosho</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="eISSN">1089-8638</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Crystallography, X-Ray</term><term>Dimerization</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Molecular Structure</term><term>Mutagenesis, Site-Directed</term><term>Nuclear Magnetic Resonance, Biomolecular (methods)</term><term>Nucleocapsid Proteins (chemistry)</term><term>Nucleocapsid Proteins (genetics)</term><term>Protein Structure, Quaternary</term><term>Protein Structure, Tertiary</term><term>Ribonucleoproteins (chemistry)</term><term>Ribonucleoproteins (metabolism)</term><term>SARS Virus (chemistry)</term><term>Severe Acute Respiratory Syndrome (virology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Nucleocapsid Proteins</term><term>Ribonucleoproteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleocapsid Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Ribonucleoproteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Nuclear Magnetic Resonance, Biomolecular</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Crystallography, X-Ray</term><term>Dimerization</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Molecular Structure</term><term>Mutagenesis, Site-Directed</term><term>Protein Structure, Quaternary</term><term>Protein Structure, Tertiary</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18561946</PMID><DateCompleted><Year>2008</Year><Month>07</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8638</ISSN><JournalIssue CitedMedium="Internet"><Volume>380</Volume><Issue>4</Issue><PubDate><Year>2008</Year><Month>Jul</Month><Day>18</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.</ArticleTitle><Pagination><MedlinePgn>608-22</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jmb.2007.11.093</ELocationID><Abstract><AbstractText>The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Takeda</LastName><ForeName>Mitsuhiro</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Chung-ke</ForeName><Initials>CK</Initials></Author><Author ValidYN="Y"><LastName>Ikeya</LastName><ForeName>Teppei</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Güntert</LastName><ForeName>Peter</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Yuan-hsiang</ForeName><Initials>YH</Initials></Author><Author ValidYN="Y"><LastName>Hsu</LastName><ForeName>Yen-lan</ForeName><Initials>YL</Initials></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Tai-huang</ForeName><Initials>TH</Initials></Author><Author ValidYN="Y"><LastName>Kainosho</LastName><ForeName>Masatsune</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>2JW8</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2007</Year><Month>12</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Mol Biol</MedlineTA><NlmUniqueID>2985088R</NlmUniqueID><ISSNLinking>0022-2836</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D019590">Nucleocapsid Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012261">Ribonucleoproteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C099602">nucleocapsid protein, Coronavirus</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019281" 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