2y1i: Difference between revisions

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-[[Image:2y1i.png|left|200px]]
-<!--
+==Crystal structure of a S-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase I from Bacillus stearothermophilus==
-The line below this paragraph, containing "STRUCTURE_2y1i", creates the "Structure Box" on the page.
+<StructureSection load='2y1i' size='340' side='right'caption='[[2y1i]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2y1i]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y1I FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.78&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBT:[3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)-PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL+DIHYDROGEN+PHOSPHATE'>PBT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
-{{STRUCTURE_2y1i|  PDB=2y1i  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2y1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y1i OCA], [https://pdbe.org/2y1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y1i RCSB], [https://www.ebi.ac.uk/pdbsum/2y1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y1i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/E1C9K5_GEOSE E1C9K5_GEOSE]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+UV light is one of the major causes of DNA damage. In spore DNA, due to an unusual packing of the genetic material, a special spore photoproduct lesion (SP lesion) is formed, which is repaired by the enzyme spore photoproduct lyase (Spl), a radical S-adenosylmethionine (SAM) enzyme. We report here the synthesis and DNA incorporation of a DNA SP lesion analogue lacking the phosphodiester backbone. The oligonucleotides were used for repair studies and they were cocrystallized with a polymerase enzyme as a template to clarify the configuration of the SP lesion and to provide information about the base-pairing properties of the lesion. The structural analysis together with repair studies allowed us to clarify the identity of the preferentially repaired lesion diastereoisomer.
-===CRYSTAL STRUCTURE OF A S-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS===
+Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion.,Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T Chemistry. 2011 Aug 22;17(35):9651-7. doi: 10.1002/chem.201100177. Epub, 2011 Jul 20. PMID:21780197<ref>PMID:21780197</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2y1i" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21780197}}, adds the Publication Abstract to the page
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21780197 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21780197}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2y1i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y1I OCA].
-==Reference==
-<ref group="xtra">PMID:021780197</ref><references group="xtra"/>
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Carell, T.]]
+[[Category: Large Structures]]
-[[Category: Heil, K.]]
+[[Category: Synthetic construct]]
-[[Category: Kneuttinger, A C.]]
+[[Category: Carell T]]
-[[Category: Mueller, M.]]
+[[Category: Heil K]]
-[[Category: Schneider, S.]]
+[[Category: Kneuttinger AC]]
-[[Category: Dna repair]]
+[[Category: Mueller M]]
-[[Category: Photolesion]]
+[[Category: Schneider S]]
-[[Category: Spore photoproduct]]
-[[Category: Transferase-dna complex]]
-[[Category: Uv lesion]]