6fbi: Difference between revisions
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==KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site== | ==KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site== | ||
<StructureSection load='6fbi' size='340' side='right' caption='[[6fbi]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='6fbi' size='340' side='right'caption='[[6fbi]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6fbi]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FBI OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6fbi]] 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=6FBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FBI 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=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]] 1.9Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6fbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fbi OCA], [https://pdbe.org/6fbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fbi RCSB], [https://www.ebi.ac.uk/pdbsum/6fbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fbi ProSAT]</span></td></tr> | ||
</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 6fbi" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6fbi" 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 in a closed, ternary complex with dGpNHpp bound in the active siteKlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site
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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