2xse

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[[Image:2xse.png|left|200px]]
 
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==The structural basis for recognition of J-base containing DNA by a novel DNA-binding domain in JBP1==
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The line below this paragraph, containing "STRUCTURE_2xse", creates the "Structure Box" on the page.
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<StructureSection load='2xse' size='340' side='right'caption='[[2xse]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2xse]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_tarentolae Leishmania tarentolae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XSE FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
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{{STRUCTURE_2xse| PDB=2xse | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xse OCA], [https://pdbe.org/2xse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xse RCSB], [https://www.ebi.ac.uk/pdbsum/2xse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xse ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/JBP1_LEITA JBP1_LEITA] Dioxygenase that catalyzes the first step of DNA base J (beta-d-glucosyl-HOMedU) biosynthesis by converting thymine to 5-hydroxymethyluracil (HOMedU). DNA base J is a hypermodified thymidine residue found in the genome of kinetoplastid parasites, which is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. Also specifically binds to base J-containing DNA (J-DNA). Involved in propagation and maintenance of DNA base J synthesis initiated by JBP2 by specifically binding already synthesized DNA base J and propagating J synthesis. Thymine dioxygenase activity and J-DNA-binding are independent functions.<ref>PMID:17389644</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (beta-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.
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===THE STRUCTURAL BASIS FOR RECOGNITION OF J-BASE CONTAINING DNA BY A NOVEL DNA-BINDING DOMAIN IN JBP1===
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The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1.,Heidebrecht T, Christodoulou E, Chalmers MJ, Jan S, Ter Riet B, Grover RK, Joosten RP, Littler D, van Luenen H, Griffin PR, Wentworth P Jr, Borst P, Perrakis A Nucleic Acids Res. 2011 Mar 16. PMID:21415010<ref>PMID:21415010</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2xse" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 21415010 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_21415010}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[2xse]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leishmania_tarentolae Leishmania tarentolae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XSE OCA].
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==Reference==
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<ref group="xtra">PMID:021415010</ref><references group="xtra"/>
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[[Category: Leishmania tarentolae]]
[[Category: Leishmania tarentolae]]
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[[Category: Thymine dioxygenase]]
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[[Category: Borst P]]
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[[Category: Borst, P.]]
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[[Category: Chalmers MJ]]
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[[Category: Chalmers, M J.]]
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[[Category: Christodoulou E]]
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[[Category: Christodoulou, E.]]
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[[Category: Griffin PR]]
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[[Category: Griffin, P R.]]
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[[Category: Grover RK]]
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[[Category: Grover, R K.]]
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[[Category: Heidebrecht T]]
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[[Category: Heidebrecht, T.]]
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[[Category: Jan S]]
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[[Category: Jan, S.]]
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[[Category: Joosten RP]]
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[[Category: Joosten, R P.]]
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[[Category: Littler D]]
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[[Category: Littler, D.]]
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[[Category: Perrakis A]]
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[[Category: Perrakis, A.]]
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[[Category: Wentworth P]]
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[[Category: Riete, B Ter.]]
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[[Category: Ter Riete B]]
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[[Category: Vanluenen, H.]]
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[[Category: VanLuenen H]]
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[[Category: Wentworth, P.]]
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[[Category: Dna-binding]]
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[[Category: Oxidoreductase]]
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Current revision

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

PDB ID 2xse

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