2fms: Difference between revisions

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-{{Seed}}
-[[Image:2fms.png|left|200px]]
-<!--
+==DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site==
-The line below this paragraph, containing "STRUCTURE_2fms", creates the "Structure Box" on the page.
+<StructureSection load='2fms' size='340' side='right'caption='[[2fms]], [[Resolution|resolution]] 2.00&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'>[[2fms]] 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=2FMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FMS 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_2fms|  PDB=2fms  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fms OCA], [https://pdbe.org/2fms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fms RCSB], [https://www.ebi.ac.uk/pdbsum/2fms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fms 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/fm/2fms_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=2fms ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide.
-===DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site===
+Magnesium-induced assembly of a complete DNA polymerase catalytic complex.,Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH Structure. 2006 Apr;14(4):757-66. PMID:16615916<ref>PMID:16615916</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2fms" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16615916}}, 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 16615916 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16615916}}
+__TOC__
+</StructureSection>
-==About this Structure==
-FMS 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=2FMS OCA].
-==Reference==
-<ref group="xtra">PMID:16615916</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Batra, V K.]]
+[[Category: Large Structures]]
-[[Category: Beard, W A.]]
+[[Category: Batra VK]]
-[[Category: Krahn, J M.]]
+[[Category: Beard WA]]
-[[Category: Pedersen, L C.]]
+[[Category: Krahn JM]]
-[[Category: Shock, D D.]]
+[[Category: Pedersen LC]]
-[[Category: Wilson, S H.]]
+[[Category: Shock DD]]
-[[Category: Nucleotidyl transferase]]
+[[Category: Wilson SH]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:42:23 2009''