1yd6: Difference between revisions

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 ==Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus caldotenax==
-<StructureSection load='1yd6' size='340' side='right' caption='[[1yd6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1yd6' size='340' side='right'caption='[[1yd6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yd6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yd6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD6 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
+</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&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ln0|1ln0]], [[1mk0|1mk0]], [[1kft|1kft]], [[1d9x|1d9x]], [[1ycz|1ycz]], [[1yd0|1yd0]], [[1yd1|1yd1]], [[1yd2|1yd2]], [[1yd3|1yd3]], [[1yd4|1yd4]], [[1yd5|1yd5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yd6 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd6 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd6 OCA], [https://pdbe.org/1yd6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd6 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd6 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UVRC_GEOKA UVRC_GEOKA] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision.[HAMAP-Rule:MF_00203]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd6_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd6_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yd6 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Nucleotide excision repair is a highly conserved DNA repair mechanism present in all kingdoms of life. The incision reaction is a critical step for damage removal and is accomplished by the UvrC protein in eubacteria. No structural information is so far available for the 3' incision reaction. Here we report the crystal structure of the N-terminal catalytic domain of UvrC at 1.5 A resolution, which catalyzes the 3' incision reaction and shares homology with the catalytic domain of the GIY-YIG family of intron-encoded homing endonucleases. The structure reveals a patch of highly conserved residues surrounding a catalytic magnesium-water cluster, suggesting that the metal binding site is an essential feature of UvrC and all GIY-YIG endonuclease domains. Structural and biochemical data strongly suggest that the N-terminal endonuclease domain of UvrC utilizes a novel one-metal mechanism to cleave the phosphodiester bond.
-Structural insights into the first incision reaction during nucleotide excision repair.,Truglio JJ, Rhau B, Croteau DL, Wang L, Skorvaga M, Karakas E, DellaVecchia MJ, Wang H, Van Houten B, Kisker C EMBO J. 2005 Mar 9;24(5):885-94. Epub 2005 Feb 3. PMID:15692561<ref>PMID:15692561</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
 *[[UvrABC|UvrABC]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus caldotenax]]
+[[Category: Large Structures]]
-[[Category: Croteau, D L.]]
+[[Category: Croteau DL]]
-[[Category: DellaVecchia, M J.]]
+[[Category: DellaVecchia MJ]]
-[[Category: Houten, B Van.]]
+[[Category: Karakas E]]
-[[Category: Karakas, E.]]
+[[Category: Kisker C]]
-[[Category: Kisker, C.]]
+[[Category: Rhau B]]
-[[Category: Rhau, B.]]
+[[Category: Skorvaga M]]
-[[Category: Skorvaga, M.]]
+[[Category: Truglio JJ]]
-[[Category: Truglio, J J.]]
+[[Category: Van Houten B]]
-[[Category: Wang, H.]]
+[[Category: Wang H]]
-[[Category: Wang, L.]]
+[[Category: Wang L]]
-[[Category: Dna binding protein]]