6q4t: Difference between revisions

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-'''Unreleased structure'''
-The entry 6q4t is ON HOLD  until Paper Publication
+==KOD DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP==
+<StructureSection load='6q4t' size='340' side='right' caption='[[6q4t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6q4t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q4T FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHZ:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>HHZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6q4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4t OCA], [http://pdbe.org/6q4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q4t RCSB], [http://www.ebi.ac.uk/pdbsum/6q4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/DPOL_THEKO DPOL_THEKO]] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Archaeal B-family DNA polymerases (DNA pols) are the driving force of cutting edge biotechnological applications like next-generation sequencing. The acceptance of chemically modified nucleotides by the DNA pols is key to these technologies. By now, no structural data are available for these DNA pols in complex with modified substrates which could build the basis for understanding interactions between the enzyme and the chemical modification and for further development of next generation nucleotides. For the first time we crystallized an exonuclease deficient variant of B-family KOD DNA pol wild-type with a modified nucleotide in a closed, ternary complex. We also crystalized the A-family DNA pol KlenTaq with the same nucleotide. The reported structural data elucidates how the protein and the DNA modulate two distinct conformations of the modification in the A- and B-family DNA pols and how these influence the processing of the modified nucleotide. Overall, this study provides first insights on how B-family DNA pols interplay with relevant modified substrates.
-Authors:
+Structure of an archaeal B-family DNA polymerase in complex with a chemically modified nucleotide.,Marx A, Kropp H, Diederichs K Angew Chem Int Ed Engl. 2019 Feb 14. doi: 10.1002/anie.201900315. PMID:30761722<ref>PMID:30761722</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6q4t" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Diederichs, K]]
+[[Category: Kropp, H M]]
+[[Category: Marx, A]]
+[[Category: Dna binding protein]]
+[[Category: Dna polymerase archaeal b-family modified nucleotide next-generation sequencing]]