[English] 日本語
![](img/lk-miru.gif)
- SASDGT2: Thymine dioxygenase J-containing DNA binding domain in complex wi... -
+
Open data
-
Basic information
Entry | ![]() |
---|---|
![]() | Thymine dioxygenase J-containing DNA binding domain in complex with J-23-DNA (JDBD:J-23-DNA)
|
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function |
Biological species | ![]() |
![]() | ![]() Title: The domain architecture of the protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity. Authors: Athanassios Adamopoulos / Tatjana Heidebrecht / Jeroen Roosendaal / Wouter G Touw / Isabelle Q Phan / Jos Beijnen / Anastassis Perrakis / ![]() ![]() Abstract: 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 ...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. |
![]() |
|
-
Structure visualization
-
Downloads & links
-Models
-
Sample
![]() | Name: Thymine dioxygenase J-containing DNA binding domain in complex with J-23-DNA (JDBD:J-23-DNA) Entity id: 898 / 899 |
---|---|
Buffer | Name: 20 mM HEPES, 200 mM NaCl, 1 mM TCEP / pH: 7.5 |
Entity #898 | Name: JDBD / Type: protein / Description: J-DNA binding domain / Formula weight: 21.244 / Num. of mol.: 1 / Source: Leishmania tarentolae / References: UniProt: Q9U6M1 Sequence: GPGPLSRLGG FSETNLMVST AVEKKKYLDS EFLLHCISAQ LLDMWKQARA RWLELVGKEW AHMLALNPER KDFLWKNQSE MNSAFFDLCE VGKQVMLGLL GKEVALPKEE QAFWIMYAVH LSAACAEELH MPEVAMSLRK LNVKLKDFNF GGTRYFKDMP PEEKKRRMER KQRIEEARRH GMP |
Entity #899 | Name: J-23-DNA / Type: DNA / Description: J-DNA (23mer) / Formula weight: 14.225 / Num. of mol.: 1 Sequence: TCGATTTGTT CATAGACTAA TACAGCTAAA CAAGTATCTG ATTATG |
-Experimental information
Beam | Instrument name: ESRF BM29 / City: Grenoble / 国: France ![]() ![]() | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm | ||||||||||||||||||||||||||||||
Scan | Measurement date: Feb 21, 2016 / Cell temperature: 4 °C / Exposure time: 1 sec. / Number of frames: 21 / Unit: 1/nm /
| ||||||||||||||||||||||||||||||
Distance distribution function P(R) |
| ||||||||||||||||||||||||||||||
Result |
|