3c5f: Difference between revisions

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-[[Image:3c5f.png|left|200px]]
-{{STRUCTURE_3c5f|  PDB=3c5f  |  SCENE=  }}
+==Structure of a binary complex of the R517A Pol lambda mutant==
+<StructureSection load='3c5f' size='340' side='right'caption='[[3c5f]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3c5f]] is a 8 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=3C5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C5F 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]] 2.25&#8491;, 2 models</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></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=3c5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c5f OCA], [https://pdbe.org/3c5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c5f RCSB], [https://www.ebi.ac.uk/pdbsum/3c5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c5f 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/c5/3c5f_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=3c5f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases. The classical idea is that simple deletions arise by strand slippage. A prime opportunity for slippage occurs during DNA synthesis, but it remains unclear how slippage is controlled during a polymerization cycle. Here, we report crystal structures and molecular dynamics simulations of mutant derivatives of DNA polymerase lambda bound to a primer-template during strand slippage. Relative to the primer strand, the template strand is in multiple conformations, indicating intermediates on the pathway to deletion mutagenesis. Consistent with these intermediates, the mutant polymerases generate single-base deletions at high rates. The results indicate that dNTP-induced template strand repositioning during conformational rearrangements in the catalytic cycle is crucial to controlling the rate of strand slippage.
-===Structure of a binary complex of the R517A Pol lambda mutant===
+Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.,Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, Kunkel TA EMBO Rep. 2008 May;9(5):459-64. Epub 2008 Mar 28. PMID:18369368<ref>PMID:18369368</ref>
-{{ABSTRACT_PUBMED_18369368}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3c5f" style="background-color:#fffaf0;"></div>
-[[3c5f]] is a 8 chain structure of [[DNA polymerase]] with 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=3C5F OCA].
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018369368</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Bebenek, K.]]
+[[Category: Large Structures]]
-[[Category: Foley, M C.]]
+[[Category: Bebenek K]]
-[[Category: Garcia-Diaz, M.]]
+[[Category: Foley MC]]
-[[Category: Kunkel, T A.]]
+[[Category: Garcia-Diaz M]]
-[[Category: Pedersen, L C.]]
+[[Category: Kunkel TA]]
-[[Category: Schlick, T.]]
+[[Category: Pedersen LC]]
-[[Category: Dna damage]]
+[[Category: Schlick T]]
-[[Category: Dna repair]]
-[[Category: Dna replication]]
-[[Category: Dna synthesis]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed dna polymerase]]
-[[Category: Helix hairpin helix]]
-[[Category: Lyase]]
-[[Category: Lyase-dna complex]]
-[[Category: Manganese]]
-[[Category: Metal-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Transferase]]