3hp6: Difference between revisions

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-{{Seed}}
-[[Image:3hp6.jpg|left|200px]]
-<!--
+==Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch==
-The line below this paragraph, containing "STRUCTURE_3hp6", creates the "Structure Box" on the page.
+<StructureSection load='3hp6' size='340' side='right'caption='[[3hp6]], [[Resolution|resolution]] 1.81&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'>[[3hp6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HP6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HP6 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]] 1.81&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=D3T:2,3-DIDEOXY-THYMIDINE-5-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3hp6|  PDB=3hp6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hp6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hp6 OCA], [https://pdbe.org/3hp6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hp6 RCSB], [https://www.ebi.ac.uk/pdbsum/3hp6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hp6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
+== 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/hp/3hp6_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=3hp6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established "open" and "closed" states. In this "ajar" conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.
-===Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch===
+The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism.,Wu EY, Beese LS J Biol Chem. 2011 Jun 3;286(22):19758-67. Epub 2011 Mar 19. PMID:21454515<ref>PMID:21454515</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3hp6" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-HP6 is a 6 chains structure with sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HP6 OCA].
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-[[Category: DNA-directed DNA polymerase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Beese, L S.]]
+[[Category: Large Structures]]
-[[Category: Wu, E Y.]]
+[[Category: Beese LS]]
-[[Category: Dna polymerase i]]
+[[Category: Wu EY]]
-[[Category: Dna replication]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed dna polymerase]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Protein-dna complex]]
-[[Category: Transferase]]
-[[Category: Transferase-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:48:08 2010''