6q4u
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 6q4u is ON HOLD Authors: Kropp, H.M., Diederichs, K., Marx, A. Description: KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydrox...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==KlenTaq 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='6q4u' size='340' side='right'caption='[[6q4u]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6q4u]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q4U FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.005Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6q4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q4u OCA], [https://pdbe.org/6q4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q4u RCSB], [https://www.ebi.ac.uk/pdbsum/6q4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q4u ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ] | ||
| + | <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. | ||
| - | + | 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Diederichs | + | <div class="pdbe-citations 6q4u" style="background-color:#fffaf0;"></div> |
| - | [[Category: Kropp | + | |
| - | [[Category: Marx | + | ==See Also== |
| + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Synthetic construct]] | ||
| + | [[Category: Thermus aquaticus]] | ||
| + | [[Category: Diederichs K]] | ||
| + | [[Category: Kropp HM]] | ||
| + | [[Category: Marx A]] | ||
Current revision
KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP
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