4j2e: Difference between revisions

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 ==RB69 DNA Polymerase L415M Ternary Complex==
-<StructureSection load='4j2e' size='340' side='right' caption='[[4j2e]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
+<StructureSection load='4j2e' size='340' side='right'caption='[[4j2e]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4j2e]] 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=4J2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J2E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4j2e]] 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=4J2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J2E 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]] 2.02&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4j2a|4j2a]], [[4j2b|4j2b]], [[4j2d|4j2d]]</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=4j2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2e OCA], [https://pdbe.org/4j2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j2e RCSB], [https://www.ebi.ac.uk/pdbsum/4j2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2e 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=4j2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2e OCA], [http://pdbe.org/4j2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j2e RCSB], [http://www.ebi.ac.uk/pdbsum/4j2e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2e ProSAT]</span></td></tr>
 </table>
 == 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 ==
-Internal 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<ref>PMID:23921641</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4j2e" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bpr69]]
+[[Category: Escherichia phage RB69]]
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Large Structures]]
-[[Category: Konigsberg, W H]]
+[[Category: Konigsberg WH]]
-[[Category: Wang, J]]
+[[Category: Wang J]]
-[[Category: Xia, S]]
+[[Category: Xia S]]
-[[Category: Dna polymerase]]
-[[Category: L415m]]
-[[Category: Polymerase]]
-[[Category: Rb69]]
-[[Category: Transferase-dna complex]]