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| | ==Ternary complex of RB69 mutant L415F wit DUMPNPP== | | ==Ternary complex of RB69 mutant L415F wit DUMPNPP== |
| - | <StructureSection load='4khq' size='340' side='right' caption='[[4khq]], [[Resolution|resolution]] 2.19Å' scene=''> | + | <StructureSection load='4khq' size='340' side='right'caption='[[4khq]], [[Resolution|resolution]] 2.19Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4khq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KHQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4khq]] 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=4KHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KHQ 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>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </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=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4khu|4khu]], [[4khw|4khw]], [[4khy|4khy]], [[4ki4|4ki4]], [[4ki6|4ki6]], [[4khs|4khs]]</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=4khq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4khq OCA], [https://pdbe.org/4khq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4khq RCSB], [https://www.ebi.ac.uk/pdbsum/4khq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4khq ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</td></tr>
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| - | <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>
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| - | <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=4khq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4khq OCA], [http://pdbe.org/4khq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4khq RCSB], [http://www.ebi.ac.uk/pdbsum/4khq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4khq ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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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| | </div> | | </div> |
| | <div class="pdbe-citations 4khq" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4khq" style="background-color:#fffaf0;"></div> |
| - | | |
| - | ==See Also== | |
| - | *[[DNA polymerase|DNA polymerase]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpr69]] | + | [[Category: Escherichia phage RB69]] |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Clausen, A R]] | + | [[Category: Clausen AR]] |
| - | [[Category: Pedersen, L C]] | + | [[Category: Pedersen LC]] |
| - | [[Category: Nucleotide]]
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| - | [[Category: Transferase-dna complex]]
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| Structural highlights
Function
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.
Publication Abstract from PubMed
Ribonucleotides 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.
References
- ↑ Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA. Structure-function analysis of ribonucleotide bypass by B family DNA replicases. 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 doi:http://dx.doi.org/10.1073/pnas.1309119110
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