1nk4: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1nk4.png|left|200px]]
-<!--
+==GUANINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
-The line below this paragraph, containing "STRUCTURE_1nk4", creates the "Structure Box" on the page.
+<StructureSection load='1nk4' size='340' side='right'caption='[[1nk4]], [[Resolution|resolution]] 1.60&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'>[[1nk4]] is a 3 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=1NK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NK4 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1nk4|  PDB=1nk4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nk4 OCA], [https://pdbe.org/1nk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nk4 RCSB], [https://www.ebi.ac.uk/pdbsum/1nk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nk4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
+== 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/nk/1nk4_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=1nk4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
-===GUANINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE===
+Structures of mismatch replication errors observed in a DNA polymerase.,Johnson SJ, Beese LS Cell. 2004 Mar 19;116(6):803-16. PMID:15035983<ref>PMID:15035983</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15035983}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1nk4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15035983 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_15035983}}
-==About this Structure==
-[[1nk4]] is a 3 chain structure of [[DNA polymerase]] with sequence 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=1NK4 OCA].
 ==See Also==
-*[[DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:15035983</ref><ref group="xtra">PMID:12649320</ref><references group="xtra"/>
+__TOC__
-[[Category: DNA-directed DNA polymerase]]
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Beese, L S.]]
+[[Category: Large Structures]]
-[[Category: Johnson, S J.]]
+[[Category: Beese LS]]
-[[Category: Dna mismatch]]
+[[Category: Johnson SJ]]
-[[Category: Dna polymerase i]]
-[[Category: Dna replication]]
-[[Category: Klenow fragment]]
-[[Category: Protein-dna complex]]
-[[Category: Transferase/dna complex]]