6fbc: Difference between revisions
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==KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.== | ==KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.== | ||
<StructureSection load='6fbc' size='340' side='right' caption='[[6fbc]], [[Resolution|resolution]] 1.54Å' scene=''> | <StructureSection load='6fbc' size='340' side='right'caption='[[6fbc]], [[Resolution|resolution]] 1.54Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6fbc]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FBC OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6fbc]] 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=6FBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FBC 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XG4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE'>XG4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.54Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4B:[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>D4B</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XG4:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE'>XG4</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=6fbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fbc OCA], [https://pdbe.org/6fbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fbc RCSB], [https://www.ebi.ac.uk/pdbsum/6fbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fbc ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 6fbc" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6fbc" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Thermus aquaticus]] | ||
[[Category: | [[Category: Diederichs K]] | ||
[[Category: | [[Category: Kropp HM]] | ||
[[Category: | [[Category: Marx A]] | ||
Latest revision as of 15:26, 9 May 2024
KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.
Structural highlights
FunctionPublication Abstract from PubMedDNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification "moves" from the 3'-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme's activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems. Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.,Kropp HM, Durr SL, Peter C, Diederichs K, Marx A Proc Natl Acad Sci U S A. 2018 Sep 17. pii: 1811518115. doi:, 10.1073/pnas.1811518115. PMID:30224478[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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