1orp: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1orp.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1orp", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1orp|  PDB=1orp  |  SCENE=  }}
-'''Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Adenine Complex'''
+==Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Adenine Complex==
+<StructureSection load='1orp' size='340' side='right'caption='[[1orp]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1orp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ORP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ORP FirstGlance]. <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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></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=1orp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1orp OCA], [https://pdbe.org/1orp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1orp RCSB], [https://www.ebi.ac.uk/pdbsum/1orp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1orp ProSAT]</span></td></tr>
+</table>
+== 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/or/1orp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1orp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.
-==Overview==
+Structure of a trapped endonuclease III-DNA covalent intermediate.,Fromme JC, Verdine GL EMBO J. 2003 Jul 1;22(13):3461-71. PMID:12840008<ref>PMID:12840008</ref>
-Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ORP OCA].
+</div>
+<div class="pdbe-citations 1orp" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structure of a trapped endonuclease III-DNA covalent intermediate., Fromme JC, Verdine GL, EMBO J. 2003 Jul 1;22(13):3461-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12840008 12840008]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-[[Category: Fromme, J C.]]
+== References ==
-[[Category: Verdine, G L.]]
+<references/>
-[[Category: Dna glycosylase]]
+__TOC__
-[[Category: Dna repair]]
+</StructureSection>
-[[Category: Iron-sulfur cluster]]
+[[Category: Geobacillus stearothermophilus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 04:12:04 2008''
+[[Category: Large Structures]]
+[[Category: Fromme JC]]
+[[Category: Verdine GL]]