1yd2: Difference between revisions

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-{{Seed}}
-[[Image:1yd2.png|left|200px]]
-<!--
+==Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y19F bound to the catalytic divalent cation==
-The line below this paragraph, containing "STRUCTURE_1yd2", creates the "Structure Box" on the page.
+<StructureSection load='1yd2' size='340' side='right'caption='[[1yd2]], [[Resolution|resolution]] 1.60&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'>[[1yd2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD2 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]] 1.6&#8491;</td></tr>
--->
+<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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_1yd2|  PDB=1yd2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd2 OCA], [https://pdbe.org/1yd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd2 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UVRC_THEMA UVRC_THEMA] 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 (By similarity).
+== 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/1yd2_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/main_output.php?pdb_ID=1yd2 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.
-===Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y19F bound to the catalytic divalent cation===
+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>
+<div class="pdbe-citations 1yd2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15692561}}, adds the Publication Abstract to the page
+*[[UvrABC 3D structures|UvrABC 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15692561 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15692561}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-YD2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD2 OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/15692561 15692561]
-[[Category: Single protein]]
 [[Category: Thermotoga maritima]]
-[[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:30:48 2008''