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

• Published in: Nucleic acids research Vol. 41; no. 7; pp. 4295 - 4306
• Main Authors: Hew, Kelly, Dahlroth, Sue-Li, Venkatachalam, Rajakannan, Nasertorabi, Fariborz, Lim, Bee Ting, Cornvik, Tobias, Nordlund, Pär
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.04.2013
• Subjects: 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
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkt082

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.