The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1.

Abstract

The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-residue domain, DB-JBP1, with 10 000-fold preference over normal DNA. The crystal structure of DB-JBP1 revealed a helix-turn-helix variant fold, a 'helical bouquet' with a 'ribbon' helix encompassing the amino acids responsible for DNA binding. Mutation of a single residue (Asp525) in the ribbon helix abrogates specificity toward J-DNA. The same mutation renders JBP1 unable to rescue the targeted deletion of endogenous JBP1 genes in Leishmania and changes its distribution in the nucleus. Based on mutational analysis and hydrogen/deuterium-exchange mass-spectrometry data, a model of JBP1 bound to J-DNA was constructed and validated by small-angle X-ray scattering data. Our results open new possibilities for targeted prevention of J-DNA recognition as a therapeutic intervention for parasitic diseases.

• Authors: Tatjana Heidebrecht, Evangelos Christodoulou, Michael J Chalmers, Sabrina Jan, Bas Ter Riet, Rajesh K Grover, Robbie P Joosten, Dene Littler, Henri van Luenen, Patrick R Griffin, Paul Wentworth Jr, Piet Borst, Anastassis Perrakis
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 39 Issue 13 Pg. 5715-28 (Jul 2011) ISSN: 1362-4962 [Electronic] England
• PMID: 21415010 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• DNA, Bacterial
• DNA-Binding Proteins
• Glucosides
• J-specific DNA-binding protein, protozoa
• Protozoan Proteins
• T-DNA
• Aspartic Acid
• 5-((glucopyranosyloxy)methyl)uracil
• Uracil
• DNA
• Arginine
• Lysine

Topics

• Amino Acid Sequence
• Arginine (chemistry)
• Aspartic Acid (chemistry)
• Crystallography, X-Ray
• DNA (chemistry)
• DNA, Bacterial (metabolism)
• DNA-Binding Proteins (chemistry, metabolism)
• Glucosides (chemistry, metabolism)
• Lysine (chemistry)
• Mass Spectrometry
• Models, Molecular
• Molecular Sequence Data
• Protein Binding
• Protein Structure, Tertiary
• Protozoan Proteins (chemistry, metabolism)
• Scattering, Small Angle
• Sequence Alignment
• Uracil (analogs & derivatives, chemistry, metabolism)
• X-Ray Diffraction