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The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif
T E Strzelecka1, G M Clore, A M Gronenborn
1Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
Background:
The Mu Ner protein is a small (74 amino acids), basic, DNA-binding protein found in phage Mu. It belongs to a class of proteins, the cro and repressor proteins, that regulate the switch from the lysogenic to the lytic state of the phage life cycle. There is no significant sequence identity between Mu Ner and the cro proteins of other phages, despite their functional similarity. In addition, there is no significant sequence identity with any other DNA-binding proteins, with the exception of Ner from the related phage D108 and the Nlp protein of Escherichia coli. As the tertiary structures of Mu Ner and these two related proteins are unknown, it is clear that a three-dimensional (3D) structure of Mu Ner is essential in order to gain insight into its mode of DNA binding.
Results:
The 3D solution structure of Mu Ner has been solved by 3D and 4D heteronuclear magnetic resonance spectroscopy. The structure consists of five alpha helices, two of which comprise a helix-turn-helix (HTH) motif. Analysis of line broadening and disappearance of crosspeaks in a 1H-15N correlation spectrum of the Mu Ner-DNA complex suggests that residues in these two helices are most likely to be in contact with the DNA.
Conclusions:
Like the functionally analogous cro proteins from phages lambda and 434, the Mu Ner protein possesses a HTH DNA recognition motif. The Ner protein from phage D108 and the Nlp protein from E. coli are likely to have very similar tertiary structures due to high amino-acid-sequence identity with Mu Ner.
Insights
The three-dimensional structure of Mu Ner protein reveals a helix-turn-helix (HTH) motif, crucial for DNA binding in phage Mu. This finding provides insights into the DNA-binding mechanism of this essential phage protein.
Area of Science:
- Structural Biology
- Molecular Biology
- Virology
Background:
- Mu Ner protein is a small, basic, DNA-binding protein from phage Mu.
- It regulates the phage life cycle, similar to cro and repressor proteins, but lacks sequence identity with other phage cro proteins.
- The tertiary structures of Mu Ner and related proteins were unknown, necessitating 3D structure determination.
Purpose of the Study:
- To determine the three-dimensional (3D) structure of the Mu Ner protein.
- To gain insight into the DNA-binding mode of Mu Ner.
Main Methods:
- 3D and 4D heteronuclear magnetic resonance (NMR) spectroscopy was used to solve the structure.
- Analysis of NMR data, including line broadening and crosspeak disappearance in a Mu Ner-DNA complex, identified DNA-interacting residues.
Main Results:
- The 3D solution structure of Mu Ner was determined.
- The structure comprises five alpha helices, including a helix-turn-helix (HTH) motif.
- NMR analysis indicated that residues within the HTH motif are involved in DNA binding.
Conclusions:
- Mu Ner protein possesses a HTH DNA recognition motif, similar to functionally analogous cro proteins.
- The Ner protein from phage D108 and Nlp protein from E. coli are predicted to have similar tertiary structures due to sequence homology.
- The determined structure provides a basis for understanding Mu Ner's DNA-binding mechanism.