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| | ==DNA Polymerase Beta E295K Soaked with dTTP== | | ==DNA Polymerase Beta E295K Soaked with dTTP== |
| - | <StructureSection load='4m9h' size='340' side='right' caption='[[4m9h]], [[Resolution|resolution]] 2.39Å' scene=''> | + | <StructureSection load='4m9h' size='340' side='right'caption='[[4m9h]], [[Resolution|resolution]] 2.39Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4m9h]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M9H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M9H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4m9h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M9H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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]] 2.394Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4m9g|4m9g]], [[4m9j|4m9j]], [[4m9l|4m9l]], [[4m9n|4m9n]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4m9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m9h OCA], [https://pdbe.org/4m9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m9h RCSB], [https://www.ebi.ac.uk/pdbsum/4m9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m9h ProSAT]</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=4m9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m9h OCA], [http://pdbe.org/4m9h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m9h RCSB], [http://www.ebi.ac.uk/pdbsum/4m9h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m9h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref> | + | [https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | DNA polymerase beta (pol beta) is responsible for gap filling synthesis during repair of damaged DNA as part of the base excision repair pathway. Human pol beta mutations were recently identified in a high percentage (~30%) of tumors. Characterization of specific cancer variants is particularly useful to further the understanding of the general mechanism of pol beta while providing context to disease contribution. We showed that expression of the carcinoma variant E295K induces cellular transformation. The poor polymerase activity exhibited by the variant was hypothesized to be caused by the destabilization of proper active site assembly by the glutamate to lysine mutation. Here we show that this variant exhibits an unusual preference for binding dCTP opposite a templating adenine over the cognate dTTP. Biochemical studies indicate that the non-cognate competes with the cognate nucleotide for binding to the polymerase active site with the non-cognate incorporation a function of higher affinity and not increased activity. In the crystal structure of the variant bound to dA:dCTP, the fingers domain closes around the mismatched base pair. Nucleotide incorporation is hindered because key residues in the polymerase active site are not properly positioned for nucleotidyl transfer. In contrast to the non-cognate dCTP, neither the cognate dTTP nor its non-hydrolyzable analog induced fingers closure, as isomorphous difference Fourier maps show that the cognate nucleotides are bound to the open state of the polymerase. Comparison to published structures provides insight into the structural rearrangements within pol beta that occur during the process of nucleotide discrimination.
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| - | The E295K cancer variant of human polymerase beta favors the mismatch conformational pathway during nucleotide selection.,Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S J Biol Chem. 2013 Oct 18. PMID:24133209<ref>PMID:24133209</ref>
| + | ==See Also== |
| - | | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4m9h" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Doublie, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Eckenroth, B E]] | + | [[Category: Doublie S]] |
| - | [[Category: Dna complex]] | + | [[Category: Eckenroth BE]] |
| - | [[Category: Dna polymerase]]
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| - | [[Category: Lyase]]
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| - | [[Category: Transferase-dna complex]]
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