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| | <SX load='6p1h' size='340' side='right' viewer='molstar' caption='[[6p1h]], [[Resolution|resolution]] 3.20Å' scene=''> | | <SX load='6p1h' size='340' side='right' viewer='molstar' caption='[[6p1h]], [[Resolution|resolution]] 3.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6p1h]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P1H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6P1H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6p1h]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] 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=6P1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P1H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POL3, CDC2, TEX1, YDL102W, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), POL32, YJR043C, J1626 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6p1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1h OCA], [https://pdbe.org/6p1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p1h RCSB], [https://www.ebi.ac.uk/pdbsum/6p1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1h ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6p1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1h OCA], [http://pdbe.org/6p1h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p1h RCSB], [http://www.ebi.ac.uk/pdbsum/6p1h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOD_YEAST DPOD_YEAST]] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity.<ref>PMID:1648480</ref> [[http://www.uniprot.org/uniprot/DPOD3_YEAST DPOD3_YEAST]] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. [[http://www.uniprot.org/uniprot/DPOD2_YEAST DPOD2_YEAST]] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair.<ref>PMID:7567461</ref> | + | [https://www.uniprot.org/uniprot/DPOD_YEAST DPOD_YEAST] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity.<ref>PMID:1648480</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | DNA polymerase delta (Poldelta) plays pivotal roles in eukaryotic DNA replication and repair. Poldelta is conserved from yeast to humans, and mutations in human Poldelta have been implicated in various cancers. Saccharomyces cerevisiae Poldelta consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 A) cryo-EM structure of yeast Poldelta holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Poldelta assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Poldelta architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.
| + | |
| | | | |
| - | Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme.,Jain R, Rice WJ, Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK Nat Struct Mol Biol. 2019 Oct;26(10):955-962. doi: 10.1038/s41594-019-0305-z., Epub 2019 Oct 3. PMID:31582849<ref>PMID:31582849</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>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6p1h" style="background-color:#fffaf0;"></div>
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Baker's yeast]] | |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Aggarwal, A K]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Jain, R]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Rice, W]] | + | [[Category: Aggarwal AK]] |
| - | [[Category: Catalysis]] | + | [[Category: Jain R]] |
| - | [[Category: Dna binding]] | + | [[Category: Rice W]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Enzyme]]
| + | |
| - | [[Category: Regulation]]
| + | |
