This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
5vbn
From Proteopedia
(Difference between revisions)
m (Protected "5vbn" [edit=sysop:move=sysop]) |
|||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit== | |
| + | <StructureSection load='5vbn' size='340' side='right' caption='[[5vbn]], [[Resolution|resolution]] 2.35Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5vbn]] is a 4 chain structure. 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> | ||
| + | </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> | ||
| + | <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=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> | ||
| + | == 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 == | ||
| + | [[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. | ||
| + | <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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 5vbn" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: DNA-directed DNA polymerase]] | ||
| + | [[Category: Babayeva, N D]] | ||
| + | [[Category: Baranovskiy, A G]] | ||
| + | [[Category: Gu, J]] | ||
| + | [[Category: Suwa, Y]] | ||
| + | [[Category: Tahirov, T H]] | ||
| + | [[Category: B-subunit]] | ||
| + | [[Category: Catalytic subunit]] | ||
| + | [[Category: Dna polymerase]] | ||
| + | [[Category: Dna polymerase epsilon]] | ||
| + | [[Category: Dna replication]] | ||
| + | [[Category: Polymerase]] | ||
| + | [[Category: Replication]] | ||
| + | [[Category: Transferase]] | ||
Revision as of 09:09, 9 August 2017
Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit
| |||||||||||
