Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition

• Published in: Nucleic acids research 2009-06, Vol.37 (10), p.3442-3451
• Main Authors: An, Young Jun, Ahn, Bo-Eun, Han, A. Reum, Kim, Hae-Mi, Chung, Kyung Min, Shin, Jung-Ho, Cho, Yoo-Bok, Roe, Jung-Hye, Cha, Sun-Shin
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - classification; Bacterial Proteins - genetics; DNA - chemistry; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - classification; DNA-Binding Proteins - genetics; Evolution, Molecular; Metals - chemistry; Models, Molecular; Mutagenesis, Site-Directed; Nickel - chemistry; Protein Binding; Protein Conformation; Protein Multimerization; Repressor Proteins - chemistry; Repressor Proteins - classification; Streptomyces coelicolor; Structural Biology; Transcription Factors - chemistry; Transcription Factors - classification; Transcription Factors - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkp198

Nur, a member of the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in Streptomyces coelicolor. Here we report the 2.4-Å resolution crystal structure of Nur. It contains a unique nickel-specific metal site in addition to a nonspecific common metal site. The identification of the 6-5-6 motif of the Nur recognition box and a Nur/DNA complex model reveals that Nur mainly interacts with terminal bases of the palindrome on complex formation. This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif. The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns. Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.