4xha: Difference between revisions
New page: '''Unreleased structure''' The entry 4xha is ON HOLD Authors: Ferrero, D.S., Buxaderas, M., Rodriguez, J.F., Verdaguer, N. Description: Common ancestor suggested by striking similariti... |
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The | ==Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with Lu3+== | ||
<StructureSection load='4xha' size='340' side='right'caption='[[4xha]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4xha]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thosea_asigna_virus Thosea asigna virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XHA FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</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>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4xha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xha OCA], [https://pdbe.org/4xha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xha RCSB], [https://www.ebi.ac.uk/pdbsum/4xha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xha ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6A562_9VIRU Q6A562_9VIRU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Thosea asigna virus (TaV), an insect virus belonging to the Permutatetraviridae family, has a positive-sense single-stranded RNA (ssRNA) genome with two overlapping open reading frames, encoding for the replicase and capsid proteins. The particular TaV replicase includes a structurally unique RNA-dependent RNA polymerase (RdRP) with a sequence permutation in the palm sub-domain, where the active site is anchored. This non-canonical arrangement of the RdRP palm is also found in double-stranded RNA viruses of the Birnaviridae family. Both virus families also share a conserved VPg sequence motif at the polymerase N-terminus which in birnaviruses appears to be used to covalently link a fraction of the replicase molecules to the 5'-end of the genomic segments. Birnavirus VPgs are presumed to be used as primers for replication initiation. Here we have solved the crystal structure of the TaV RdRP, the first non-canonical RdRP of a ssRNA virus, in its apo- form and bound to different substrates. The enzyme arranges as a stable dimer maintained by mutual interactions between the active site cleft of one molecule and the flexible N-terminal tail of the symmetrically related RdRP. The latter, partially mimicking the RNA template backbone, is involved in regulating the polymerization activity. As expected from previous sequence-based bioinformatics predictions, the overall architecture of the TaV enzyme shows important resemblances with birnavirus polymerases. In addition, structural comparisons and biochemical analyses reveal unexpected similarities between the TaV RdRP and those of Flaviviruses. In particular, a long loop protruding from the thumb domain towards the central enzyme cavity appears to act as a platform for de novo initiation of RNA replication. Our findings strongly suggest an unexpected evolutionary relationship between the RdRPs encoded by these distant ssRNA virus groups. | |||
The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases.,Ferrero DS, Buxaderas M, Rodriguez JF, Verdaguer N PLoS Pathog. 2015 Dec 1;11(12):e1005265. doi: 10.1371/journal.ppat.1005265., eCollection 2015 Dec. PMID:26625123<ref>PMID:26625123</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 4xha" style="background-color:#fffaf0;"></div> | ||
[[Category: Buxaderas | |||
[[Category: | ==See Also== | ||
[[Category: Rodriguez | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thosea asigna virus]] | |||
[[Category: Buxaderas M]] | |||
[[Category: Ferrero DS]] | |||
[[Category: Rodriguez JF]] | |||
[[Category: Verdaguer N]] | |||
Latest revision as of 14:29, 9 May 2024
Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with Lu3+Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with Lu3+
Structural highlights
FunctionPublication Abstract from PubMedThosea asigna virus (TaV), an insect virus belonging to the Permutatetraviridae family, has a positive-sense single-stranded RNA (ssRNA) genome with two overlapping open reading frames, encoding for the replicase and capsid proteins. The particular TaV replicase includes a structurally unique RNA-dependent RNA polymerase (RdRP) with a sequence permutation in the palm sub-domain, where the active site is anchored. This non-canonical arrangement of the RdRP palm is also found in double-stranded RNA viruses of the Birnaviridae family. Both virus families also share a conserved VPg sequence motif at the polymerase N-terminus which in birnaviruses appears to be used to covalently link a fraction of the replicase molecules to the 5'-end of the genomic segments. Birnavirus VPgs are presumed to be used as primers for replication initiation. Here we have solved the crystal structure of the TaV RdRP, the first non-canonical RdRP of a ssRNA virus, in its apo- form and bound to different substrates. The enzyme arranges as a stable dimer maintained by mutual interactions between the active site cleft of one molecule and the flexible N-terminal tail of the symmetrically related RdRP. The latter, partially mimicking the RNA template backbone, is involved in regulating the polymerization activity. As expected from previous sequence-based bioinformatics predictions, the overall architecture of the TaV enzyme shows important resemblances with birnavirus polymerases. In addition, structural comparisons and biochemical analyses reveal unexpected similarities between the TaV RdRP and those of Flaviviruses. In particular, a long loop protruding from the thumb domain towards the central enzyme cavity appears to act as a platform for de novo initiation of RNA replication. Our findings strongly suggest an unexpected evolutionary relationship between the RdRPs encoded by these distant ssRNA virus groups. The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases.,Ferrero DS, Buxaderas M, Rodriguez JF, Verdaguer N PLoS Pathog. 2015 Dec 1;11(12):e1005265. doi: 10.1371/journal.ppat.1005265., eCollection 2015 Dec. PMID:26625123[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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