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| | ==NMR Solution Structure of the nuclease domain from the Replicator Initiator Protein from porcine circovirus PCV2== | | ==NMR Solution Structure of the nuclease domain from the Replicator Initiator Protein from porcine circovirus PCV2== |
| - | <StructureSection load='2hw0' size='340' side='right'caption='[[2hw0]], [[NMR_Ensembles_of_Models | 31 NMR models]]' scene=''> | + | <StructureSection load='2hw0' size='340' side='right'caption='[[2hw0]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2hw0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pcv2 Pcv2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HW0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2hw0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Porcine_circovirus_2 Porcine circovirus 2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HW0 FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rep, ORF1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85708 PCV2])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2hw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hw0 OCA], [https://pdbe.org/2hw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hw0 RCSB], [https://www.ebi.ac.uk/pdbsum/2hw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hw0 ProSAT]</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=2hw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hw0 OCA], [https://pdbe.org/2hw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hw0 RCSB], [https://www.ebi.ac.uk/pdbsum/2hw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hw0 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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pcv2]] | + | [[Category: Porcine circovirus 2]] |
| - | [[Category: Byeon, I L]] | + | [[Category: Byeon IL]] |
| - | [[Category: Campos-Olivas, R]] | + | [[Category: Campos-Olivas R]] |
| - | [[Category: Gronenborn, A M]] | + | [[Category: Gronenborn AM]] |
| - | [[Category: Gronenborn, B]] | + | [[Category: Gronenborn B]] |
| - | [[Category: Vega-Rocha, S]] | + | [[Category: Vega-Rocha S]] |
| - | [[Category: Alpha+beta]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Replication]]
| + | |
| Structural highlights
Function
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.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Circoviruses are the smallest circular single-stranded DNA viruses able to replicate in mammalian cells. Essential to their replication is the replication initiator, or Rep protein that initiates the rolling circle replication (RCR) of the viral genome. Here we report the NMR solution three-dimensional structure of the endonuclease domain from the Rep protein of porcine circovirus type 2 (PCV2), the causative agent of postweaning multisystemic wasting syndrome in swine. The domain comprises residues 12-112 of the full-length protein and exhibits the fold described previously for the Rep protein of the representative geminivirus tomato yellow leaf curl Sardinia virus. The structure, however, differs significantly in some secondary structure elements that decorate the central five-stranded beta-sheet, including the replacement of a beta-hairpin by an alpha-helix in PCV2 Rep. The identification of the divalent metal binding site was accomplished by following the paramagnetic broadening of NMR amide signals upon Mn(2+) titration. The site comprises three conserved acidic residues on the exposed face of the central beta-sheet. For the 1:1 complex of the PCV2 Rep nuclease domain with a 22mer double-stranded DNA oligonucleotide chemical shift mapping allowed the identification of the DNA binding site on the protein and aided in constructing a model of the protein/DNA complex.
Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2.,Vega-Rocha S, Byeon IJ, Gronenborn B, Gronenborn AM, Campos-Olivas R J Mol Biol. 2007 Mar 23;367(2):473-87. Epub 2007 Jan 9. PMID:17275023[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cheung AK. The essential and nonessential transcription units for viral protein synthesis and DNA replication of porcine circovirus type 2. Virology. 2003 Sep 1;313(2):452-9. PMID:12954212 doi:10.1016/s0042-6822(03)00373-8
- ↑ Cheung AK. Specific functions of the Rep and Rep׳ proteins of porcine circovirus during copy-release and rolling-circle DNA replication. Virology. 2015 Jul;481:43-50. PMID:25768890 doi:10.1016/j.virol.2015.01.004
- ↑ Vega-Rocha S, Byeon IJ, Gronenborn B, Gronenborn AM, Campos-Olivas R. Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2. J Mol Biol. 2007 Mar 23;367(2):473-87. Epub 2007 Jan 9. PMID:17275023 doi:10.1016/j.jmb.2007.01.002
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