6wdz
From Proteopedia
(Difference between revisions)
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| - | ==== | + | ==Porcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site== |
| - | <StructureSection load='6wdz' size='340' side='right'caption='[[6wdz]]' scene=''> | + | <StructureSection load='6wdz' size='340' side='right'caption='[[6wdz]], [[Resolution|resolution]] 2.03Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6wdz]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Porcine_circovirus_2 Porcine circovirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WDZ FirstGlance]. <br> |
| - | </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=6wdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdz OCA], [https://pdbe.org/6wdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wdz RCSB], [https://www.ebi.ac.uk/pdbsum/6wdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdz ProSAT]</span></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]] 2.03Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=6wdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wdz OCA], [https://pdbe.org/6wdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wdz RCSB], [https://www.ebi.ac.uk/pdbsum/6wdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wdz ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/REP_PCV2 REP_PCV2] Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3' in the intergenic region of the genome, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, and nucleotidyl transferase.<ref>PMID:12954212</ref> <ref>PMID:25768890</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications. | ||
| + | |||
| + | Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering.,Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limon-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR Nucleic Acids Res. 2021 Jan 25;49(2):1046-1064. doi: 10.1093/nar/gkaa1248. PMID:33410911<ref>PMID:33410911</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6wdz" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Porcine circovirus 2]] |
| + | [[Category: Evans III RL]] | ||
| + | [[Category: Gordon WR]] | ||
| + | [[Category: Litzau LA]] | ||
| + | [[Category: Nelson A]] | ||
| + | [[Category: Shi K]] | ||
| + | [[Category: Tompkins K]] | ||
Current revision
Porcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
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