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| | <StructureSection load='4m8o' size='340' side='right'caption='[[4m8o]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='4m8o' size='340' side='right'caption='[[4m8o]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4m8o]] is a 3 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=4M8O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M8O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4m8o]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M8O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M8O 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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=C38:5-IODO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C38</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=C38:5-IODO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C38</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POL2, DUN2, YNL262W, N0825 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4m8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m8o OCA], [https://pdbe.org/4m8o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m8o RCSB], [https://www.ebi.ac.uk/pdbsum/4m8o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m8o 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=4m8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m8o OCA], [http://pdbe.org/4m8o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m8o RCSB], [http://www.ebi.ac.uk/pdbsum/4m8o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m8o ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOE_YEAST DPOE_YEAST]] DNA polymerase epsilon (DNA polymerase II) 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:12124389</ref> | + | [https://www.uniprot.org/uniprot/DPOE_YEAST DPOE_YEAST] DNA polymerase epsilon (DNA polymerase II) 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:12124389</ref> |
| | <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 4m8o" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4m8o" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hogg, M]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Johansson, E]] | + | [[Category: Hogg M]] |
| - | [[Category: Osterman, P]] | + | [[Category: Johansson E]] |
| - | [[Category: Sauer-Eriksson, A E]] | + | [[Category: Osterman P]] |
| - | [[Category: Dna polymerase b type]]
| + | [[Category: Sauer-Eriksson AE]] |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Dna synthesis]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nucleotidyltransferase]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Transferase dna complex]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
4m8o is a 3 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.2Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DPOE_YEAST DNA polymerase epsilon (DNA polymerase II) 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.[1]
Publication Abstract from PubMed
DNA polymerase varepsilon (Pol varepsilon) is a high-fidelity polymerase that has been shown to participate in leading-strand synthesis during DNA replication in eukaryotic cells. We present here a ternary structure of the catalytic core of Pol varepsilon (142 kDa) from Saccharomyces cerevisiae in complex with DNA and an incoming nucleotide. This structure provides information about the selection of the correct nucleotide and the positions of amino acids that might be critical for proofreading activity. Pol varepsilon has the highest fidelity among B-family polymerases despite the absence of an extended beta-hairpin loop that is required for high-fidelity replication by other B-family polymerases. Moreover, the catalytic core has a new domain that allows Pol varepsilon to encircle the nascent double-stranded DNA. Altogether, the structure provides an explanation for the high processivity and high fidelity of leading-strand DNA synthesis in eukaryotes.
Structural basis for processive DNA synthesis by yeast DNA polymerase varepsilon.,Hogg M, Osterman P, Bylund GO, Ganai RA, Lundstrom EB, Sauer-Eriksson AE, Johansson E Nat Struct Mol Biol. 2014 Jan;21(1):49-55. doi: 10.1038/nsmb.2712. Epub 2013 Dec , 1. PMID:24292646[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Shimizu K, Hashimoto K, Kirchner JM, Nakai W, Nishikawa H, Resnick MA, Sugino A. Fidelity of DNA polymerase epsilon holoenzyme from budding yeast Saccharomyces cerevisiae. J Biol Chem. 2002 Oct 4;277(40):37422-9. Epub 2002 Jul 17. PMID:12124389 doi:http://dx.doi.org/10.1074/jbc.M204476200
- ↑ Hogg M, Osterman P, Bylund GO, Ganai RA, Lundstrom EB, Sauer-Eriksson AE, Johansson E. Structural basis for processive DNA synthesis by yeast DNA polymerase varepsilon. Nat Struct Mol Biol. 2014 Jan;21(1):49-55. doi: 10.1038/nsmb.2712. Epub 2013 Dec , 1. PMID:24292646 doi:http://dx.doi.org/10.1038/nsmb.2712
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