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==RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==
==RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair==
<StructureSection load='4dto' size='340' side='right' caption='[[4dto]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
<StructureSection load='4dto' size='340' side='right'caption='[[4dto]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4dto]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DTO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DTO FirstGlance]. <br>
<table><tr><td colspan='2'>[[4dto]] 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=4DTO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DTO 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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dtj|4dtj]], [[4dtm|4dtm]], [[4dtn|4dtn]], [[4dtp|4dtp]], [[4dtr|4dtr]], [[4dts|4dts]], [[4dtu|4dtu]], [[4dtx|4dtx]], [[4du1|4du1]], [[4du3|4du3]], [[4du4|4du4]]</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=4dto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dto OCA], [https://pdbe.org/4dto PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dto RCSB], [https://www.ebi.ac.uk/pdbsum/4dto PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dto 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 Enterobacteria phage RB69])</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=4dto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dto OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dto RCSB], [http://www.ebi.ac.uk/pdbsum/4dto PDBsum]</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;">
== Publication Abstract from PubMed ==
During DNA synthesis base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base-pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the Penultimate Base-pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The incorporation efficiency for incoming dNTPs opposite an abasic site varied between 2 and 210 fold depending on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporations were consistent with specific features of base-stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex and the incorporation efficiency of incoming dNTPs is reduced.
 
Contribution of Partial Charge Interactions and Base-Stacking to the Efficiency of Primer-Extension at and beyond Abasic Sites in DNA.,Xia S, Vashishtha AK, Bulkley D, Eom SH, Wang J, Konigsberg WH Biochemistry. 2012 May 25. PMID:22630605<ref>PMID:22630605</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[DNA polymerase|DNA polymerase]]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Escherichia phage RB69]]
[[Category: Enterobacteria phage rb69]]
[[Category: Large Structures]]
[[Category: Konigsberg, W H]]
[[Category: Konigsberg WH]]
[[Category: Wang, J]]
[[Category: Wang J]]
[[Category: Xia, S]]
[[Category: Xia S]]
[[Category: Abasic site]]
[[Category: Datp]]
[[Category: Rb69pol]]
[[Category: Thf]]
[[Category: Transferase-dna complex]]

Latest revision as of 13:56, 1 March 2024

RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pairRB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair

Structural highlights

4dto is a 3 chain structure with sequence from Escherichia phage RB69. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

4dto, resolution 2.05Å

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