6isf: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Structure of 9N-I DNA polymerase incorporation with dT in the active site== | |||
<StructureSection load='6isf' size='340' side='right'caption='[[6isf]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6isf]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ISF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ISF FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></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=6isf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6isf OCA], [http://pdbe.org/6isf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6isf RCSB], [http://www.ebi.ac.uk/pdbsum/6isf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6isf ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
It was reported in 1995 that T7 and Taq DNA polymerases possess 3'-esterase activity, but without follow-up studies. Here we report that the 3'-esterase activity is intrinsic to the Thermococcus sp. 9 degrees N DNA polymerase, and that it can be developed into a continuous method for DNA sequencing with dNTP analogs carrying a 3'-ester with a fluorophore. We first show that 3'-esterified dNTP can be incorporated into a template-primer DNA, and solve the crystal structures of the reaction intermediates and products. Then we show that the reaction can occur continuously, modulated by active site residues Tyr409 and Asp542. Finally, we use 5'-FAM-labeled primer and esterified dNTP with a dye to show that the reaction can proceed to ca. 450 base pairs, and that the intermediates of many individual steps can be identified. The results demonstrate the feasibility of a 3'-editing based DNA sequencing method that could find practical applications after further optimization. | |||
Thermococcus sp. 9 degrees N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.,LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD Commun Biol. 2019 Jun 20;2:224. doi: 10.1038/s42003-019-0458-7. eCollection 2019. PMID:31240262<ref>PMID:31240262</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Chang, W | <div class="pdbe-citations 6isf" style="background-color:#fffaf0;"></div> | ||
[[Category: Linwu, S | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: DNA-directed DNA polymerase]] | |||
[[Category: Large Structures]] | |||
[[Category: Chang, W H]] | |||
[[Category: Linwu, S W]] | |||
[[Category: Maestre-Reyna, M]] | [[Category: Maestre-Reyna, M]] | ||
[[Category: Tsai, M D]] | |||
[[Category: Tu, Y H]] | |||
[[Category: Dna polymerase]] | |||
[[Category: Transferase-dna complex]] | |||
Revision as of 18:26, 28 August 2019
Structure of 9N-I DNA polymerase incorporation with dT in the active siteStructure of 9N-I DNA polymerase incorporation with dT in the active site
Structural highlights
Publication Abstract from PubMedIt was reported in 1995 that T7 and Taq DNA polymerases possess 3'-esterase activity, but without follow-up studies. Here we report that the 3'-esterase activity is intrinsic to the Thermococcus sp. 9 degrees N DNA polymerase, and that it can be developed into a continuous method for DNA sequencing with dNTP analogs carrying a 3'-ester with a fluorophore. We first show that 3'-esterified dNTP can be incorporated into a template-primer DNA, and solve the crystal structures of the reaction intermediates and products. Then we show that the reaction can occur continuously, modulated by active site residues Tyr409 and Asp542. Finally, we use 5'-FAM-labeled primer and esterified dNTP with a dye to show that the reaction can proceed to ca. 450 base pairs, and that the intermediates of many individual steps can be identified. The results demonstrate the feasibility of a 3'-editing based DNA sequencing method that could find practical applications after further optimization. Thermococcus sp. 9 degrees N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.,LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD Commun Biol. 2019 Jun 20;2:224. doi: 10.1038/s42003-019-0458-7. eCollection 2019. PMID:31240262[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||