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| | <StructureSection load='4fly' size='340' side='right'caption='[[4fly]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='4fly' size='340' side='right'caption='[[4fly]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fly]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FLY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fly]] 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=4FLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FLY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</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=4fly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fly OCA], [https://pdbe.org/4fly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fly RCSB], [https://www.ebi.ac.uk/pdbsum/4fly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fly ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4flt|4flt]], [[4flu|4flu]], [[4flv|4flv]], [[4flw|4flw]], [[4flx|4flx]], [[4flz|4flz]], [[4fm0|4fm0]], [[4fm1|4fm1]], [[4fm2|4fm2]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polI, pol, PYRAB17200, PAB1128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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=4fly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fly OCA], [http://pdbe.org/4fly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fly RCSB], [http://www.ebi.ac.uk/pdbsum/4fly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fly ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DPOL_PYRAB DPOL_PYRAB] |
| | <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 4fly" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4fly" style="background-color:#fffaf0;"></div> |
| - | | |
| - | ==See Also== | |
| - | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrab]] | + | [[Category: Pyrococcus abyssi GE5]] |
| - | [[Category: Delarue, M]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Gouge, J]] | + | [[Category: Delarue M]] |
| - | [[Category: Dna binding]] | + | [[Category: Gouge J]] |
| - | [[Category: Dna polymerase]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
Function
DPOL_PYRAB
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gouge J, Ralec C, Henneke G, Delarue M. Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase. J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479 doi:http://dx.doi.org/10.1016/j.jmb.2012.07.025
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