4j2a: Difference between revisions
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==RB69 DNA Polymerase L415A Ternary Complex== | ==RB69 DNA Polymerase L415A Ternary Complex== | ||
<StructureSection load='4j2a' size='340' side='right' caption='[[4j2a]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='4j2a' size='340' side='right'caption='[[4j2a]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4j2a]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4j2a]] 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=4J2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J2A 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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene | </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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=4j2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2a OCA], [https://pdbe.org/4j2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j2a RCSB], [https://www.ebi.ac.uk/pdbsum/4j2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2a 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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</div> | </div> | ||
<div class="pdbe-citations 4j2a" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4j2a" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia phage RB69]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Konigsberg | [[Category: Konigsberg WH]] | ||
[[Category: Wang | [[Category: Wang J]] | ||
[[Category: Xia | [[Category: Xia S]] | ||
Revision as of 00:26, 17 November 2022
RB69 DNA Polymerase L415A Ternary ComplexRB69 DNA Polymerase L415A Ternary Complex
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 PubMedInternal cavities are a common feature of many proteins, often having profound effects on the dynamics of their interactions with substrate and binding partners. RB69 DNA polymerase (pol) has a hydrophobic cavity right below the nucleotide binding pocket at the tip of highly conserved L415 side chain. Replacement of this residue with Gly or Met in other B family pols resulted in higher mutation rates. When similar substitutions for L415 were introduced into RB69pol, only L415A and L415G had dramatic effects on pre-steady-state kinetic parameters, reducing base selectivity by several hundred fold. On the other hand, the L415M variant behaved like the wild-type. Using a novel tC(o)-tCnitro Forster Resonance Energy Transfer (FRET) assay, we were able to show that the partition of the primer terminus between pol and exonuclease (exo) domains was compromised with the L415A and L415G mutants, but not with the L415M variant. These results could be rationalized by changes in their structures as determined by high resolution X-ray crystallography. Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.,Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH Nucleic Acids Res. 2013 Oct;41(19):9077-89. doi: 10.1093/nar/gkt674. Epub 2013, Aug 5. PMID:23921641[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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