6ur4: Difference between revisions
New page: '''Unreleased structure''' The entry 6ur4 is ON HOLD Authors: Zhagn, W., Lelyveld, V.S., Szostak, J.W. Description: Crystal structure of fragment DNA polymerase I from Bacillus stearot... |
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==DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and 3'-amino primer== | |||
<StructureSection load='6ur4' size='340' side='right'caption='[[6ur4]], [[Resolution|resolution]] 2.25Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ur4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] 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=6UR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UR4 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]] 2.25Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C42:3-AMINO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C42</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=6ur4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ur4 OCA], [https://pdbe.org/6ur4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ur4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ur4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ur4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D9N168_GEOSE D9N168_GEOSE] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3'-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3'-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3'-->P5' phosphoramidate (NP) bonds, no such internucleotide linkages are known to occur in nature. Here, we report that 3'-amino terminated primers are, in fact, slowly extended by the DNA polymerase from B. stearothermophilus in a template-directed manner. When its cofactor is Ca(2+) rather than Mg(2+), the reaction is fivefold faster, permitting multiple turnover NP bond formation to yield NP-DNA strands from the corresponding 3'-amino-2',3'-dideoxynucleoside 5'-triphosphates. A single active site mutation further enhances the rate of NP-DNA synthesis by an additional 21-fold. We show that DNA-dependent NP-DNA polymerase activity depends on conserved active site residues and propose a likely mechanism for this activity based on a series of crystal structures of bound complexes. Our results significantly broaden the catalytic scope of polymerase activity and suggest the feasibility of a genetic transition between native nucleic acids and NP-DNA. | |||
Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.,Lelyveld VS, Zhang W, Szostak JW Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7276-7283. doi:, 10.1073/pnas.1922400117. Epub 2020 Mar 18. PMID:32188786<ref>PMID:32188786</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6ur4" style="background-color:#fffaf0;"></div> | ||
[[Category: Szostak | |||
[[Category: | ==See Also== | ||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Geobacillus stearothermophilus]] | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Lelyveld VS]] | |||
[[Category: Szostak JW]] | |||
[[Category: Zhang W]] | |||
Latest revision as of 10:56, 11 October 2023
DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and 3'-amino primerDNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and 3'-amino primer
Structural highlights
FunctionPublication Abstract from PubMedAll known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3'-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3'-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3'-->P5' phosphoramidate (NP) bonds, no such internucleotide linkages are known to occur in nature. Here, we report that 3'-amino terminated primers are, in fact, slowly extended by the DNA polymerase from B. stearothermophilus in a template-directed manner. When its cofactor is Ca(2+) rather than Mg(2+), the reaction is fivefold faster, permitting multiple turnover NP bond formation to yield NP-DNA strands from the corresponding 3'-amino-2',3'-dideoxynucleoside 5'-triphosphates. A single active site mutation further enhances the rate of NP-DNA synthesis by an additional 21-fold. We show that DNA-dependent NP-DNA polymerase activity depends on conserved active site residues and propose a likely mechanism for this activity based on a series of crystal structures of bound complexes. Our results significantly broaden the catalytic scope of polymerase activity and suggest the feasibility of a genetic transition between native nucleic acids and NP-DNA. Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.,Lelyveld VS, Zhang W, Szostak JW Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7276-7283. doi:, 10.1073/pnas.1922400117. Epub 2020 Mar 18. PMID:32188786[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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