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Yorodumi- SASDGQ2: Thymine dioxygenase lacking the JDNA binding domain Delta-JDBD (Δ... -
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-Basic information
Entry | Database: SASBDB / ID: SASDGQ2 |
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Sample | Thymine dioxygenase lacking the JDNA binding domain Delta-JDBD (Δ-JDBD)
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Function / homology | Function and homology information thymine dioxygenase / thymine dioxygenase activity / base J metabolic process / DNA binding / nucleus / metal ion binding Similarity search - Function |
Biological species | Leismania tarentolae |
Citation | Journal: J Biol Chem / Year: 2019 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. |
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-Structure visualization
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-Sample
Sample | Name: Thymine dioxygenase lacking the JDNA binding domain Delta-JDBD (Δ-JDBD) Specimen concentration: 10.3 mg/ml |
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Buffer | Name: 20 mM HEPES, 200 mM NaCl, 1 mM TCEP / pH: 7.5 |
Entity #897 | Name: Δ-JDBD / Type: protein / Description: Delta-JDBD / Formula weight: 72.468 / Num. of mol.: 1 / Source: Leismania tarentolae / References: UniProt: Q9U6M1 Sequence: GPGEPDSKKV KLDIFNFPTT RETRTPEEVA ESYAEAVKSH PFYDNVHSVV DFYDSGTIKD GRGQIIGVVL REALPKYAAS MASELLTSAA VRTSLRSMMF GGEPPLSGIA GYFDYRGSPV ELKSRKTSFT YEHEAAWPAV FPVVDYVSEI YRHVAPERWK AQNDAIPDLV ...Sequence: GPGEPDSKKV KLDIFNFPTT RETRTPEEVA ESYAEAVKSH PFYDNVHSVV DFYDSGTIKD GRGQIIGVVL REALPKYAAS MASELLTSAA VRTSLRSMMF GGEPPLSGIA GYFDYRGSPV ELKSRKTSFT YEHEAAWPAV FPVVDYVSEI YRHVAPERWK AQNDAIPDLV RIHGTPFSTL TINSRFRTAS HTDVGDFDAG YSCIACLDGQ FKGLALSFDD FGINVLLQPR DVMIFDSHHF HSNTEVELSF SGEDWKRLTC VFYYRAALGE PASYAEYQRR LEKSKTDTRF TPVVHHVRVK ENGTSVNRPS PVYPISQSPF WVPMVAHCLQ HCASAAQCVH EAMTADGSRL AEMMFGESLS TSDGIPLRGE DEKVKANGDS TPRSGSHEKR ANWLTNDSFD YQTEDCVIDY AQHKWVLPAL HAKEVTKTVR TGELPTTERV VRVLVVIPDP QSKLENVDCK LEVPDMVGSS SEWERLMSSP AVHRVLSAAQ RNLQLPDSVT HGNVQTHFAF HSTLPTDIYD FVVLQHVLSR IPDDAQASAY IRRAAALCSG CLFVVETDVQ CRQYYTLKYS IRCSYDTVAP LFFQQLHRVC YGTKTARVRT KGELESLIPT VCCARYKLQG SPLNTTVHVV SPFPSCEVQN LSSALCDRA |
-Experimental information
Beam | Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 2.872 mm | |||||||||||||||||||||||||||||||||
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Detector | Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm | |||||||||||||||||||||||||||||||||
Scan | Title: Thymine dioxygenase lacking the JDNA binding domain Delta-JDBD (Δ-JDBD) Measurement date: Feb 21, 2016 / Cell temperature: 4 °C / Exposure time: 1 sec. / Number of frames: 50 / Unit: 1/nm /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 881 /
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Result | Type of curve: sec /
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