8BBM

DNA binding domain of J-DNA Binding Protein 1 (JBP1)

Summary for 8BBM

• Entry DOI: 10.2210/pdb8bbm/pdb
• Descriptor: Thymine dioxygenase JBP1 (2 entities in total)
• Functional Keywords: j-dna binding protein, jbp1, oxidoreductase
• Biological source: Leishmania tarentolae
• Total number of polymer chains: 1
• Total formula weight: 20537.34

Authors

de Vries, I.,Joosten, R.P.,Perrakis, A. (deposition date: 2022-10-13, release date: 2022-11-09, Last modification date: 2024-02-07)

Primary citation

de Vries, I.,Ammerlaan, D.,Heidebrecht, T.,Celie, P.H.,Geerke, D.P.,Joosten, R.P.,Perrakis, A.
Distant sequence regions of JBP1 contribute to J-DNA binding.
Life Sci Alliance, 6:-, 2023

PubMed Abstract: Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

PubMed: 37328191
DOI: 10.26508/lsa.202302150

Experimental method

X-RAY DIFFRACTION (1.95 Å)