4ki6: Difference between revisions
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==Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position== | ==Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position== | ||
<StructureSection load='4ki6' size='340' side='right' caption='[[4ki6]], [[Resolution|resolution]] 2.55Å' scene=''> | <StructureSection load='4ki6' size='340' side='right'caption='[[4ki6]], [[Resolution|resolution]] 2.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ki6]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4ki6]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KI6 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ki6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ki6 OCA], [https://pdbe.org/4ki6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ki6 RCSB], [https://www.ebi.ac.uk/pdbsum/4ki6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ki6 ProSAT]</span></td></tr> | ||
< | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia phage RB69]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Clausen | [[Category: Clausen AR]] | ||
[[Category: Pedersen | [[Category: Pedersen LC]] | ||
Latest revision as of 18:59, 20 September 2023
Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 positionTernary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position
Structural highlights
FunctionDPOL_BPR69 This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Publication Abstract from PubMedRibonucleotides are frequently incorporated into DNA during replication, they are normally removed, and failure to remove them results in replication stress. This stress correlates with DNA polymerase (Pol) stalling during bypass of ribonucleotides in DNA templates. Here we demonstrate that stalling by yeast replicative Pols delta and epsilon increases as the number of consecutive template ribonucleotides increases from one to four. The homologous bacteriophage RB69 Pol also stalls during ribonucleotide bypass, with a pattern most similar to that of Pol epsilon. Crystal structures of an exonuclease-deficient variant of RB69 Pol corresponding to multiple steps in single ribonucleotide bypass reveal that increased stalling is associated with displacement of Tyr391 and an unpreferred C2'-endo conformation for the ribose. Even less efficient bypass of two consecutive ribonucleotides in DNA correlates with similar movements of Tyr391 and displacement of one of the ribonucleotides along with the primer-strand DNA backbone. These structure-function studies have implications for cellular signaling by ribonucleotides, and they may be relevant to replication stress in cells defective in ribonucleotide excision repair, including humans suffering from autoimmune disease associated with RNase H2 defects. Structure-function analysis of ribonucleotide bypass by B family DNA replicases.,Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16802-7. doi:, 10.1073/pnas.1309119110. Epub 2013 Sep 30. PMID:24082122[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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