2aq4: Difference between revisions

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-[[Image:2aq4.gif|left|200px]]
-<!--
+==Ternary complex of the catalytic core of REV1 with DNA and dCTP.==
-The line below this paragraph, containing "STRUCTURE_2aq4", creates the "Structure Box" on the page.
+<StructureSection load='2aq4' size='340' side='right'caption='[[2aq4]], [[Resolution|resolution]] 2.32&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'>[[2aq4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AQ4 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]] 2.32&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2aq4|  PDB=2aq4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aq4 OCA], [https://pdbe.org/2aq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aq4 RCSB], [https://www.ebi.ac.uk/pdbsum/2aq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aq4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
+== 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/aq/2aq4_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=2aq4 ConSurf].
+<div style="clear:both"></div>
-'''Ternary complex of the catalytic core of REV1 with DNA and dCTP.'''
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
-==Overview==
+<references/>
-The Rev1 DNA polymerase is highly specialized for the incorporation of C opposite template G. We present here the crystal structure of yeast Rev1 bound to template G and incoming 2'-deoxycytidine 5'-triphosphate (dCTP), which reveals that the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. Template G and incoming dCTP do not pair with each other. Instead, the template G is evicted from the DNA helix, and it makes optimal hydrogen bonds with a segment of Rev1. Also, unlike other DNA polymerases, incoming dCTP pairs with an arginine rather than the templating base, which ensures the incorporation of dCTP over other incoming nucleotides. This mechanism provides an elegant means for promoting proficient and error-free synthesis through N2-adducted guanines that obstruct replication.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-AQ4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AQ4 OCA].
-==Reference==
-Rev1 employs a novel mechanism of DNA synthesis using a protein template., Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Science. 2005 Sep 30;309(5744):2219-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16195463 16195463]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Aggarwal AK]]
-[[Category: Aggarwal, A K.]]
+[[Category: Johnson RE]]
-[[Category: Johnson, R E.]]
+[[Category: Nair DT]]
-[[Category: Nair, D T.]]
+[[Category: Prakash L]]
-[[Category: Prakash, L.]]
+[[Category: Prakash S]]
-[[Category: Prakash, S.]]
-[[Category: G-loop]]
-[[Category: N-digit]]
-[[Category: Pad]]
-[[Category: Polymerase]]
-[[Category: Rev1]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:20:02 2008''