6ur4: Difference between revisions

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-'''Unreleased structure'''
-The entry 6ur4 is ON HOLD
+==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]] 2.25&Aring;' 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]] 2.25&#8491;</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'--&gt;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.
-Authors: Zhagn, W., Lelyveld, V.S., Szostak, J.W.
+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>
-Description: Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with DNA template and 3'-amino primer
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Zhagn, W]]
+<div class="pdbe-citations 6ur4" style="background-color:#fffaf0;"></div>
-[[Category: Szostak, J.W]]
-[[Category: Lelyveld, V.S]]
+==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]]