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| | <StructureSection load='5vbn' size='340' side='right'caption='[[5vbn]], [[Resolution|resolution]] 2.35Å' scene=''> | | <StructureSection load='5vbn' size='340' side='right'caption='[[5vbn]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5vbn]] 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5vbn]] 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VBN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.35Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLE2, DPE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), POLE, POLE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [https://pdbe.org/5vbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [https://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn 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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [http://pdbe.org/5vbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [http://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | == Disease == | |
| - | [[http://www.uniprot.org/uniprot/DPOE1_HUMAN DPOE1_HUMAN]] Facial dysmorphism - immunodeficiency - livedo - short stature. Disease susceptibility is associated with variations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. | |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOE2_HUMAN DPOE2_HUMAN]] Participates in DNA repair and in chromosomal DNA replication. [[http://www.uniprot.org/uniprot/DPOE1_HUMAN DPOE1_HUMAN]] Participates in DNA repair and in chromosomal DNA replication. | + | [https://www.uniprot.org/uniprot/DPOE2_HUMAN DPOE2_HUMAN] Participates in DNA repair and in chromosomal DNA replication. |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The eukaryotic B-family DNA polymerases include four members, Polalpha, Poldelta, Pol, and Polzeta, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polalpha and Poldelta/Polzeta have been reported; the former within the primosome and separately with CTD, and the latter with the N-terminal domain (NTD) of the C-subunit. Here we present the crystal structure of the human Pol B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well-defined electron density for p261C and the phosphodiesterase (PDE) and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 NTD and for the linker connecting it to the PDE domain. Similar to Polalpha, p261C contains a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 A2 Comparative structural analysis of p59-p261C with the corresponding Polalpha complex revealed significant differences between the B-subunits and CTDs as well as their interaction interfaces. The B-subunit of Poldelta/Polzeta also substantially differs from B-subunits of either Polalpha or Pol. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.
| + | |
| - | | + | |
| - | Crystal structure of the human Pol B-subunit in complex with the C-terminal domain of the catalytic subunit.,Baranovskiy AG, Gu J, Babayeva ND, Kurinov I, Pavlov YI, Tahirov TH J Biol Chem. 2017 Jul 26. pii: jbc.M117.792705. doi: 10.1074/jbc.M117.792705. PMID:28747437<ref>PMID:28747437</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5vbn" style="background-color:#fffaf0;"></div>
| + | |
| | | | |
| | ==See Also== | | ==See Also== |
| | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Human]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Babayeva, N D]] | + | [[Category: Babayeva ND]] |
| - | [[Category: Baranovskiy, A G]] | + | [[Category: Baranovskiy AG]] |
| - | [[Category: Gu, J]] | + | [[Category: Gu J]] |
| - | [[Category: Suwa, Y]] | + | [[Category: Suwa Y]] |
| - | [[Category: Tahirov, T H]] | + | [[Category: Tahirov TH]] |
| - | [[Category: B-subunit]]
| + | |
| - | [[Category: Catalytic subunit]]
| + | |
| - | [[Category: Dna polymerase]]
| + | |
| - | [[Category: Dna polymerase epsilon]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Polymerase]]
| + | |
| - | [[Category: Replication]]
| + | |
| - | [[Category: Transferase]]
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