|
|
| Line 3: |
Line 3: |
| | <SX load='6t8h' size='340' side='right' viewer='molstar' caption='[[6t8h]], [[Resolution|resolution]] 3.77Å' scene=''> | | <SX load='6t8h' size='340' side='right' viewer='molstar' caption='[[6t8h]], [[Resolution|resolution]] 3.77Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6t8h]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993] and [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T8H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T8H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6t8h]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi], [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5] 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=6T8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T8H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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">Electron Microscopy, [[Resolution|Resolution]] 3.77Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pcn, PYRAB13790, PAB1465 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB]), polB, PYRAB01210, PAB2266 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=6t8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t8h OCA], [https://pdbe.org/6t8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t8h RCSB], [https://www.ebi.ac.uk/pdbsum/6t8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t8h 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=6t8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t8h OCA], [http://pdbe.org/6t8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t8h RCSB], [http://www.ebi.ac.uk/pdbsum/6t8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t8h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PCNA_PYRAB PCNA_PYRAB]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication (By similarity). Regulates activity of NucS endonuclease and prevents non-specific cleavage.[HAMAP-Rule:MF_00317]<ref>PMID:22431731</ref> [[http://www.uniprot.org/uniprot/DP2S_PYRAB DP2S_PYRAB]] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3' to 5' direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity). | + | [https://www.uniprot.org/uniprot/PCNA_PYRAB PCNA_PYRAB] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication (By similarity). Regulates activity of NucS endonuclease and prevents non-specific cleavage.[HAMAP-Rule:MF_00317]<ref>PMID:22431731</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 20: |
Line 19: |
| | </div> | | </div> |
| | <div class="pdbe-citations 6t8h" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6t8h" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | + | *[[Proliferating cell nuclear antigen 3D structures|Proliferating cell nuclear antigen 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Pyrococcus abyssi erauso et al. 1993]] | |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrab]] | + | [[Category: Pyrococcus abyssi]] |
| - | [[Category: Beaufet, I Hugonneau]] | + | [[Category: Pyrococcus abyssi GE5]] |
| - | [[Category: Carroni, M]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Delarue, M]] | + | [[Category: Carroni M]] |
| - | [[Category: England, P]] | + | [[Category: Delarue M]] |
| - | [[Category: Lindhal, E]] | + | [[Category: England P]] |
| - | [[Category: Madru, C]] | + | [[Category: Hugonneau Beaufet I]] |
| - | [[Category: Pehau-Arnaudet, G]] | + | [[Category: Lindhal E]] |
| - | [[Category: Raia, P]] | + | [[Category: Madru C]] |
| - | [[Category: Sauguet, L]] | + | [[Category: Pehau-Arnaudet G]] |
| - | [[Category: Dp1]]
| + | [[Category: Raia P]] |
| - | [[Category: Dp2]]
| + | [[Category: Sauguet L]] |
| - | [[Category: Pcna]]
| + | |
| - | [[Category: Pip-box]]
| + | |
| - | [[Category: Pold]]
| + | |
| - | [[Category: Replication]]
| + | |
| Structural highlights
Function
PCNA_PYRAB Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication (By similarity). Regulates activity of NucS endonuclease and prevents non-specific cleavage.[HAMAP-Rule:MF_00317][1]
Publication Abstract from PubMed
Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD-PCNA complex from Pyrococcus abyssi at 3.77 A. Using an integrative structural biology approach - combining cryo-EM, X-ray crystallography, protein-protein interaction measurements, and activity assays - we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polalpha replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication.
Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.,Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L Nat Commun. 2020 Mar 27;11(1):1591. doi: 10.1038/s41467-020-15392-9. PMID:32221299[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Creze C, Ligabue A, Laurent S, Lestini R, Laptenok SP, Khun J, Vos MH, Czjzek M, Myllykallio H, Flament D. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. J Biol Chem. 2012 May 4;287(19):15648-60. doi: 10.1074/jbc.M112.346361. Epub 2012, Mar 19. PMID:22431731 doi:http://dx.doi.org/10.1074/jbc.M112.346361
- ↑ Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun. 2020 Mar 27;11(1):1591. doi: 10.1038/s41467-020-15392-9. PMID:32221299 doi:http://dx.doi.org/10.1038/s41467-020-15392-9
|
