|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==RB69 DNA polymerase ternary complex with dG/dT at position n-2 of primer/tempLate duplex== | | ==RB69 DNA polymerase ternary complex with dG/dT at position n-2 of primer/tempLate duplex== |
| - | <StructureSection load='4m3z' size='340' side='right' caption='[[4m3z]], [[Resolution|resolution]] 1.84Å' scene=''> | + | <StructureSection load='4m3z' size='340' side='right'caption='[[4m3z]], [[Resolution|resolution]] 1.84Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4m3z]] 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=4M3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M3Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4m3z]] 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=4M3Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M3Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.84Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4m3r|4m3r]], [[4m3t|4m3t]], [[4m3u|4m3u]], [[4m3w|4m3w]], [[4m3x|4m3x]], [[4m3y|4m3y]], [[4m41|4m41]], [[4m42|4m42]], [[4m45|4m45]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4m3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m3z OCA], [https://pdbe.org/4m3z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m3z RCSB], [https://www.ebi.ac.uk/pdbsum/4m3z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m3z ProSAT]</span></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=4m3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m3z OCA], [http://pdbe.org/4m3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m3z RCSB], [http://www.ebi.ac.uk/pdbsum/4m3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m3z 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;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn2+ indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affect by its microenvironment, we determined ten structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states.
| + | |
| - | | + | |
| - | Mispairs with Watson-Crick Base-pair Geometry Observed in Ternary Complexes of an RB69 DNA Polymerase Variant.,Xia S, Konigsberg WH Protein Sci. 2014 Jan 24. doi: 10.1002/pro.2434. PMID:24458997<ref>PMID:24458997</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 4m3z" style="background-color:#fffaf0;"></div>
| + | |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[DNA polymerase|DNA polymerase]] | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpr69]] | + | [[Category: Escherichia phage RB69]] |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Konigsberg, W H]] | + | [[Category: Konigsberg WH]] |
| - | [[Category: Xia, S]] | + | [[Category: Xia S]] |
| - | [[Category: Dg/dt]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: N-2]]
| + | |
| - | [[Category: Quadruple]]
| + | |
| - | [[Category: Rb69]]
| + | |
| - | [[Category: Rb69 pol]]
| + | |
