4fm2: Difference between revisions
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==Pyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsDNA, in edition mode== | |||
<StructureSection load='4fm2' size='340' side='right'caption='[[4fm2]], [[Resolution|resolution]] 2.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4fm2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5] 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=4FM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FM2 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]] 2.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4fm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fm2 OCA], [https://pdbe.org/4fm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fm2 RCSB], [https://www.ebi.ac.uk/pdbsum/4fm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fm2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DPOL_PYRAB DPOL_PYRAB] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Euryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3A and 2.9A resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5. | |||
Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.,Gouge J, Ralec C, Henneke G, Delarue M J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479<ref>PMID:22902479</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4fm2" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
[[ | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: Pyrococcus abyssi | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Pyrococcus abyssi GE5]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Delarue M]] | |||
[[Category: Gouge J]] | |||
Latest revision as of 11:20, 9 October 2024
Pyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsDNA, in edition modePyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsDNA, in edition mode
Structural highlights
FunctionPublication Abstract from PubMedEuryarchaeal polymerase B can recognize deaminated bases on the template strand, effectively stalling the replication fork 4nt downstream the modified base. Using Pyrococcus abyssi DNA B family polymerase (PabPolB), we investigated the discrimination between deaminated and natural nucleotide(s) by primer extension assays, electrophoretic mobility shift assays, and X-ray crystallography. Structures of complexes between the protein and DNA duplexes with either a dU or a dH in position +4 were solved at 2.3A and 2.9A resolution, respectively. The PabPolB is found in the editing mode. A new metal binding site has been uncovered below the base-checking cavity where the +4 base is flipped out; it is fully hydrated in an octahedral fashion and helps guide the strongly kinked template strand. Four other crystal structures with each of the canonical bases were also solved in the editing mode, and the presence of three nucleotides in the exonuclease site caused a shift in the coordination state of its metal A from octahedral to tetrahedral. Surprisingly, we find that all canonical bases also enter the base-checking pocket with very small differences in the binding geometry and in the calculated binding free energy compared to deaminated ones. To explain how this can lead to stalling of the replication fork, the full catalytic pathway and its branches must be taken into account, during which the base is checked several times. Our results strongly suggest a switch from elongation to editing modes right after nucleotide insertion when the modified base is at position +5. Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.,Gouge J, Ralec C, Henneke G, Delarue M J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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