|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6q1m' size='340' side='right'caption='[[6q1m]], [[Resolution|resolution]] 1.24Å' scene=''> | | <StructureSection load='6q1m' size='340' side='right'caption='[[6q1m]], [[Resolution|resolution]] 1.24Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6q1m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Wdv Wdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q1M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Q1M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6q1m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Wheat_dwarf_virus Wheat dwarf virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q1M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.24Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">repA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10834 WDV])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=6q1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q1m OCA], [http://pdbe.org/6q1m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q1m RCSB], [http://www.ebi.ac.uk/pdbsum/6q1m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q1m 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=6q1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q1m OCA], [https://pdbe.org/6q1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q1m RCSB], [https://www.ebi.ac.uk/pdbsum/6q1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q1m ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/REP_WDVS REP_WDVS] Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific region at the genome origin of replication. It introduces an endonucleolytic nick within the conserved sequence 5'-TAATATTAC-3' in the intergenic region of the genome present in all geminiviruses, 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, nucleotidyl transferase, ATPase and helicase activities. Acts as an inhibitor of C-sense gene transcription (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 22: |
Line 24: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Wdv]] | + | [[Category: Wheat dwarf virus]] |
| - | [[Category: Everett, B A]] | + | [[Category: Evans III RL]] |
| - | [[Category: Gordon, W R]] | + | [[Category: Everett BA]] |
| - | [[Category: III, R L.Evans]] | + | [[Category: Gordon WR]] |
| - | [[Category: Litzau, L A]] | + | [[Category: Litzau LA]] |
| - | [[Category: Shi, K]] | + | [[Category: Shi K]] |
| - | [[Category: Tompkins, K]] | + | [[Category: Tompkins K]] |
| - | [[Category: Huh motif]]
| + | |
| - | [[Category: Huh-tag]]
| + | |
| - | [[Category: Rep domain]]
| + | |
| - | [[Category: Replication]]
| + | |
| - | [[Category: Single stranded dna]]
| + | |
| - | [[Category: Ssdna]]
| + | |
| - | [[Category: Ssdna binding]]
| + | |
| - | [[Category: Viral protein]]
| + | |
| Structural highlights
Function
REP_WDVS Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific region at the genome origin of replication. It introduces an endonucleolytic nick within the conserved sequence 5'-TAATATTAC-3' in the intergenic region of the genome present in all geminiviruses, 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, nucleotidyl transferase, ATPase and helicase activities. Acts as an inhibitor of C-sense gene transcription (By similarity).
Publication Abstract from PubMed
The Rep domain of Wheat dwarf virus (WDV Rep) is an HUH endonuclease involved in rolling-circle replication. HUH endonucleases coordinate a metal ion to enable the nicking of a specific ssDNA sequence and the subsequent formation of an intermediate phosphotyrosine bond. This covalent protein-ssDNA adduct makes HUH endonucleases attractive fusion tags (HUH-tags) in a diverse number of biotechnological applications. Solving the structure of an HUH endonuclease in complex with ssDNA will provide critical information about ssDNA recognition and sequence specificity, thus enabling rationally engineered protein-DNA interactions that are programmable. The structure of the WDV Rep domain reported here was solved in the apo state from a crystal diffracting to 1.24 A resolution and represents an initial step in the direction of solving the structure of a protein-ssDNA complex.
Crystal structure of the Wheat dwarf virus Rep domain.,Everett BA, Litzau LA, Tompkins K, Shi K, Nelson A, Aihara H, Evans Iii RL, Gordon WR Acta Crystallogr F Struct Biol Commun. 2019 Dec 1;75(Pt 12):744-749. doi:, 10.1107/S2053230X19015796. Epub 2019 Nov 27. PMID:31797816[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Everett BA, Litzau LA, Tompkins K, Shi K, Nelson A, Aihara H, Evans Iii RL, Gordon WR. Crystal structure of the Wheat dwarf virus Rep domain. Acta Crystallogr F Struct Biol Commun. 2019 Dec 1;75(Pt 12):744-749. doi:, 10.1107/S2053230X19015796. Epub 2019 Nov 27. PMID:31797816 doi:http://dx.doi.org/10.1107/S2053230X19015796
|
