3c2m: Difference between revisions

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-{{Seed}}
-[[Image:3c2m.png|left|200px]]
-<!--
+==Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site==
-The line below this paragraph, containing "STRUCTURE_3c2m", creates the "Structure Box" on the page.
+<StructureSection load='3c2m' size='340' side='right'caption='[[3c2m]], [[Resolution|resolution]] 2.15&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'>[[3c2m]] 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=3C2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2M 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]] 2.15&#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=F2A:2-DEOXY-5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE'>F2A</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_3c2m|  PDB=3c2m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2m OCA], [https://pdbe.org/3c2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2m RCSB], [https://www.ebi.ac.uk/pdbsum/3c2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</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/c2/3c2m_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=3c2m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substituting Mn(2+) for Mg(2+) significantly decreases the fidelity of DNA synthesis. The structures reveal that the enzyme is in a closed conformation like that observed with a matched Watson-Crick base pair. The incorrect dAMPCPP binds in a conformation identical to that observed with the correct nucleotide. To accommodate the incorrect nucleotide and closed protein conformation, the template strand in the vicinity of the active site has shifted upstream over 3 A, removing the coding base from the active site and generating an abasic templating pocket. The primer terminus rotates as its complementary template base is repositioned. This rotation moves O3' of the primer terminus away from the alpha-phosphate of the incoming nucleotide, thereby deterring misincorporation.
-===Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site===
+Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.,Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH Mol Cell. 2008 May 9;30(3):315-24. PMID:18471977<ref>PMID:18471977</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3c2m" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-C2M is a 4 chains structure of sequences 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=3C2M OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Batra, V K.]]
+[[Category: Large Structures]]
-[[Category: Beard, W A.]]
+[[Category: Batra VK]]
-[[Category: Pedersen, L C.]]
+[[Category: Beard WA]]
-[[Category: Shock, D D.]]
+[[Category: Pedersen LC]]
-[[Category: Wilson, S H.]]
+[[Category: Shock DD]]
-[[Category: Dna damage]]
+[[Category: Wilson SH]]
-[[Category: Dna polymerase]]
-[[Category: Dna repair]]
-[[Category: Dna replication]]
-[[Category: Dna synthesis]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed dna polymerase]]
-[[Category: Lyase]]
-[[Category: Lyase/dna complex]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Misincorporation]]
-[[Category: Nucleotidyl transferase]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nucleus]]
-[[Category: Polymorphism]]
-[[Category: Sodium]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:20:07 2009''