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TitleThe domain architecture of the protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity.
Journal, issue, pagesJ Biol Chem, Vol. 294, Issue 34, Page 12815-12825, Year 2019
Publish dateAug 23, 2019
AuthorsAthanassios Adamopoulos / Tatjana Heidebrecht / Jeroen Roosendaal / Wouter G Touw / Isabelle Q Phan / Jos Beijnen / Anastassis Perrakis /
PubMed AbstractJ-DNA-binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-d-glucosyl-hydroxymethyluracil), an epigenetic modification of thymidine (T) confined to pathogenic ...J-DNA-binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-d-glucosyl-hydroxymethyluracil), an epigenetic modification of thymidine (T) confined to pathogenic protozoa such as and JBP1 has two known functional domains: an N-terminal T hydroxylase (TH) homologous to the 5-methylcytosine hydroxylase domain in TET proteins and a J-DNA-binding domain (JDBD) that resides in the middle of JBP1. Here, we show that removing JDBD from JBP1 results in a soluble protein (Δ-JDBD) with the N- and C-terminal regions tightly associated together in a well-ordered structure. We found that this Δ-JDBD domain retains TH activity but displays a 15-fold lower apparent rate of hydroxylation compared with JBP1. Small-angle X-ray scattering (SAXS) experiments on JBP1 and JDBD in the presence or absence of J-DNA and on Δ-JDBD enabled us to generate low-resolution three-dimensional models. We conclude that Δ-JDBD, and not the N-terminal region of JBP1 alone, is a distinct folding unit. Our SAXS-based model supports the notion that binding of JDBD specifically to J-DNA can facilitate T hydroxylation 12-14 bp downstream on the complementary strand of the J-recognition site. We postulate that insertion of the JDBD module into the Δ-JDBD scaffold during evolution provided a mechanism that synergized J recognition and T hydroxylation, ensuring inheritance of base J in specific sequence patterns following DNA replication in kinetoplastid parasites.
External linksJ Biol Chem / PubMed:31292194 / PubMed Central
MethodsSAS (X-ray synchrotron)
Structure data

SASDGP2: Thymine dioxygenase full length J-DNA binding protein (JBP1)
Method: SAXS/SANS

SASDGQ2: Thymine dioxygenase lacking the JDNA binding domain Delta-JDBD (Δ-JDBD)
Method: SAXS/SANS

SASDGR2: Thymine dioxygenase J-containing DNA binding domain (JDBD)
Method: SAXS/SANS

SASDGS2: J-23-DNA (J-DNA (23mer))
Method: SAXS/SANS

SASDGT2: Thymine dioxygenase J-containing DNA binding domain in complex with J-23-DNA (JDBD:J-23-DNA)
Method: SAXS/SANS

SASDGU2: Thymine dioxygenase full length J-DNA binding protein in complex with J-23-DNA (JBP1:J-23-DNA)
Method: SAXS/SANS

Source
  • Leishmania tarentolae (eukaryote)
  • Leismania tarentolae

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