The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor
Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-...
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Published in | Nucleic acids research Vol. 41; no. 7; pp. 4295 - 4306 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
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Oxford University Press
01.04.2013
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Abstract | Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1's function has remained uncertain. To provide insights into the function of the vIRF-1 DBD, we have determined the crystal structure of it in complex with DNA and in its apo-form. Using a thermal stability shift assay (TSSA), we show that the vIRF-1 DBD binds DNA, whereas full-length vIRF-1 does not, suggesting a cis-acting regulatory mechanism in similarity to human IRFs. The complex structure of vIRF-1 DBD reveals interactions with the DNA backbone and the positioning of two arginines for specific recognition in the major grove. A superimposition with human IRF-3 reveals a similar positioning of the two specificity-determining arginines, and additional TSSAs indicate binding of vIRF-1 to an IRF-3 operator consensus sequence. The results from this study, therefore, provide support that vIRF-1 has evolved to bind DNA and plays a role in DNA binding in the context of transcriptional regulation and might act on some of the many operator sequences controlled by human IRF-3. |
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AbstractList | Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1's function has remained uncertain. To provide insights into the function of the vIRF-1 DBD, we have determined the crystal structure of it in complex with DNA and in its apo-form. Using a thermal stability shift assay (TSSA), we show that the vIRF-1 DBD binds DNA, whereas full-length vIRF-1 does not, suggesting a cis-acting regulatory mechanism in similarity to human IRFs. The complex structure of vIRF-1 DBD reveals interactions with the DNA backbone and the positioning of two arginines for specific recognition in the major grove. A superimposition with human IRF-3 reveals a similar positioning of the two specificity-determining arginines, and additional TSSAs indicate binding of vIRF-1 to an IRF-3 operator consensus sequence. The results from this study, therefore, provide support that vIRF-1 has evolved to bind DNA and plays a role in DNA binding in the context of transcriptional regulation and might act on some of the many operator sequences controlled by human IRF-3. Kaposi’s sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1’s function has remained uncertain. To provide insights into the function of the vIRF-1 DBD, we have determined the crystal structure of it in complex with DNA and in its apo-form. Using a thermal stability shift assay (TSSA), we show that the vIRF-1 DBD binds DNA, whereas full-length vIRF-1 does not, suggesting a cis -acting regulatory mechanism in similarity to human IRFs. The complex structure of vIRF-1 DBD reveals interactions with the DNA backbone and the positioning of two arginines for specific recognition in the major grove. A superimposition with human IRF-3 reveals a similar positioning of the two specificity-determining arginines, and additional TSSAs indicate binding of vIRF-1 to an IRF-3 operator consensus sequence. The results from this study, therefore, provide support that vIRF-1 has evolved to bind DNA and plays a role in DNA binding in the context of transcriptional regulation and might act on some of the many operator sequences controlled by human IRF-3. |
Author | Hew, Kelly Venkatachalam, Rajakannan Dahlroth, Sue-Li Lim, Bee Ting Nordlund, Pär Cornvik, Tobias Nasertorabi, Fariborz |
AuthorAffiliation | 1 Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore and 2 Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 11, Sweden |
AuthorAffiliation_xml | – name: 1 Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore and 2 Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 11, Sweden |
Author_xml | – sequence: 1 givenname: Kelly surname: Hew fullname: Hew, Kelly organization: Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore – sequence: 2 givenname: Sue-Li surname: Dahlroth fullname: Dahlroth, Sue-Li – sequence: 3 givenname: Rajakannan surname: Venkatachalam fullname: Venkatachalam, Rajakannan – sequence: 4 givenname: Fariborz surname: Nasertorabi fullname: Nasertorabi, Fariborz – sequence: 5 givenname: Bee Ting surname: Lim fullname: Lim, Bee Ting – sequence: 6 givenname: Tobias surname: Cornvik fullname: Cornvik, Tobias – sequence: 7 givenname: Pär surname: Nordlund fullname: Nordlund, Pär |
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Snippet | Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even... Kaposi’s sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even... |
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SubjectTerms | Cell- och molekylärbiologi Crystallography, X-Ray DNA - chemistry DNA - metabolism Interferon Regulatory Factors - chemistry Interferon Regulatory Factors - metabolism Medicin och hälsovetenskap Medicinska och farmaceutiska grundvetenskaper Models, Molecular Protein Folding Protein Structure, Tertiary Structural Biology Viral Proteins - chemistry Viral Proteins - metabolism |
Title | The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor |
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