2bcq: Difference between revisions

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-{{Seed}}
-[[Image:2bcq.png|left|200px]]
-<!--
+==DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp==
-The line below this paragraph, containing "STRUCTURE_2bcq", creates the "Structure Box" on the page.
+<StructureSection load='2bcq' size='340' side='right'caption='[[2bcq]], [[Resolution|resolution]] 1.65&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'>[[2bcq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BCQ 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]] 1.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>
-{{STRUCTURE_2bcq|  PDB=2bcq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bcq OCA], [https://pdbe.org/2bcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bcq RCSB], [https://www.ebi.ac.uk/pdbsum/2bcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bcq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</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/bc/2bcq_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=2bcq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misaligned intermediates stabilized by correct base pairing that support polymerization. We report here crystal structures of human DNA polymerase lambda, which frequently generates deletion mutations, bound to such intermediates. Each contains an extrahelical template nucleotide upstream of the active site. Surprisingly, the extra nucleotide, even when combined with an adjacent mismatch, does not perturb polymerase active site geometry, which is indistinguishable from that for correctly aligned strands. These structures reveal how pol lambda can polymerize on substrates with minimal homology during repair of double-strand breaks and represent strand-slippage intermediates consistent with Streisinger's classical hypothesis. They are thus relevant to the origin of single-base deletions, a class of mutations that can confer strong biological phenotypes.
-===DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp===
+Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase.,Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA Cell. 2006 Jan 27;124(2):331-42. PMID:16439207<ref>PMID:16439207</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bcq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16439207}}, 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 16439207 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16439207}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BCQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BCQ OCA].
-==Reference==
-Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase., Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA, Cell. 2006 Jan 27;124(2):331-42. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16439207 16439207]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bebenek, K.]]
+[[Category: Bebenek K]]
-[[Category: Garcia-Diaz, M.]]
+[[Category: Garcia-Diaz M]]
-[[Category: Krahn, J M.]]
+[[Category: Krahn JM]]
-[[Category: Kunkel, T A.]]
+[[Category: Kunkel TA]]
-[[Category: Pedersen, L C.]]
+[[Category: Pedersen LC]]
-[[Category: Deletion]]
-[[Category: Extrahelical]]
-[[Category: Misalignment]]
-[[Category: Mutagenesis]]
-[[Category: Mutation]]
-[[Category: Slippage]]
-[[Category: Streisinger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 08:22:19 2008''