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| | <StructureSection load='5ltn' size='340' side='right'caption='[[5ltn]], [[Resolution|resolution]] 1.88Å' scene=''> | | <StructureSection load='5ltn' size='340' side='right'caption='[[5ltn]], [[Resolution|resolution]] 1.88Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ltn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lcmv Lcmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LTN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LTN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ltn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lymphocytic_choriomeningitis_mammarenavirus Lymphocytic choriomeningitis mammarenavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LTN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LTN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=XI7:2-4-DIOXO-4-PHENYLBUTANOIC+ACID'>XI7</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]] 1.88Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ltf|5ltf]], [[5t2t|5t2t]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=XI7:2-4-DIOXO-4-PHENYLBUTANOIC+ACID'>XI7</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L, KUE_IGS320002 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11623 LCMV])</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=5ltn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ltn OCA], [https://pdbe.org/5ltn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ltn RCSB], [https://www.ebi.ac.uk/pdbsum/5ltn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ltn ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ltn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ltn OCA], [http://pdbe.org/5ltn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ltn RCSB], [http://www.ebi.ac.uk/pdbsum/5ltn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ltn ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A059U381_9VIRU A0A059U381_9VIRU]] RNA-dependent RNA polymerase which is responsible for replication and transcription of the viral RNA genome. During transcription, synthesizes 4 subgenomic RNAs, and assures their capping by a cap-snatching mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. The 3'-end of subgenomic mRNAs molecules are heterogeneous and not polyadenylated. The replicase function is to direct synthesis of antigenomic and genomic RNA which are encapsidated and non capped. As a consequence of the use of the same enzyme for both transcription and replication, these mechanisms need to be well coordinated. These processes may be regulated by proteins N and Z in a dose-dependent manner.[PIRNR:PIRNR000836] | + | [https://www.uniprot.org/uniprot/L_LYCVA L_LYCVA] RNA-dependent RNA polymerase which is responsible for replication and transcription of the viral RNA genome. During transcription, synthesizes 4 subgenomic RNAs, and assures their capping by a cap-snatching mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. The 3'-end of subgenomic mRNAs molecules are heterogeneous and not polyadenylated. The replicase function is to direct synthesis of antigenomic and genomic RNA which are encapsidated and non capped. As a consequence of the use of the same enzyme for both transcription and replication, these mechanisms need to be well coordinated. These processes may be regulated by proteins N and Z in a dose-dependent manner.<ref>PMID:7682625</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lcmv]] | + | [[Category: Lymphocytic choriomeningitis mammarenavirus]] |
| - | [[Category: RNA-directed RNA polymerase]]
| + | [[Category: Alvarez K]] |
| - | [[Category: Alvarez, K]] | + | [[Category: Canard B]] |
| - | [[Category: Canard, B]] | + | [[Category: Ferron F]] |
| - | [[Category: Ferron, F]] | + | [[Category: Saez-Ayala M]] |
| - | [[Category: Saez-Ayala, M]] | + | [[Category: Yekwa EL]] |
| - | [[Category: Yekwa, E L]] | + | |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Lcmv arenavirus dpba]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
5ltn is a 2 chain structure with sequence from Lymphocytic choriomeningitis mammarenavirus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.88Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
L_LYCVA RNA-dependent RNA polymerase which is responsible for replication and transcription of the viral RNA genome. During transcription, synthesizes 4 subgenomic RNAs, and assures their capping by a cap-snatching mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. The 3'-end of subgenomic mRNAs molecules are heterogeneous and not polyadenylated. The replicase function is to direct synthesis of antigenomic and genomic RNA which are encapsidated and non capped. As a consequence of the use of the same enzyme for both transcription and replication, these mechanisms need to be well coordinated. These processes may be regulated by proteins N and Z in a dose-dependent manner.[1]
Publication Abstract from PubMed
The Arenaviridae family, together with the Bunyaviridae and Orthomyxoviridae families, is one of the three negative-stranded RNA viral families that encode an endonuclease in their genome. The endonuclease domain is at the N-terminus of the L protein, a multifunctional protein that includes the RNA-dependent RNA polymerase. The synthesis of mRNA in arenaviruses is a process that is primed by capped nucleotides that are 'stolen' from the cellular mRNA by the endonuclease domain in cooperation with other domains of the L protein. This molecular mechanism has been demonstrated previously for the endonuclease of the prototype Lymphocytic choriomeningitis virus (LCMV). However, the mode of action of this enzyme is not fully understood as the original structure did not contain catalytic metal ions. The pivotal role played by the cap-snatching process in the life cycle of the virus and the highly conserved nature of the endonuclease domain make it a target of choice for the development of novel antiviral therapies. Here, the binding affinities of two diketo-acid (DKA) compounds (DPBA and L-742,001) for the endonuclease domain of LCMV were evaluated using biophysical methods. X-ray structures of the LCMV endonuclease domain with catalytic ions in complex with these two compounds were determined, and their efficacies were assessed in an in vitro endonuclease-activity assay. Based on these data and computational simulation, two new DKAs were synthesized. The LCMV endonuclease domain exhibits a good affinity for these DKAs, making them a good starting point for the design of arenavirus endonuclease inhibitors. In addition to providing the first example of an X-ray structure of an arenavirus endonuclease incorporating a ligand, this study provides a proof of concept that the design of optimized inhibitors against the arenavirus endonuclease is possible.
Crystal structures of Lymphocytic choriomeningitis virus endonuclease domain complexed with diketo-acid ligands.,Saez-Ayala M, Yekwa EL, Carcelli M, Canard B, Alvarez K, Ferron F IUCrJ. 2018 Feb 22;5(Pt 2):223-235. doi: 10.1107/S2052252518001021. eCollection, 2018 Mar 1. PMID:29765612[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Meyer BJ, Southern PJ. Concurrent sequence analysis of 5' and 3' RNA termini by intramolecular circularization reveals 5' nontemplated bases and 3' terminal heterogeneity for lymphocytic choriomeningitis virus mRNAs. J Virol. 1993 May;67(5):2621-7. PMID:7682625
- ↑ Saez-Ayala M, Yekwa EL, Carcelli M, Canard B, Alvarez K, Ferron F. Crystal structures of Lymphocytic choriomeningitis virus endonuclease domain complexed with diketo-acid ligands. IUCrJ. 2018 Feb 22;5(Pt 2):223-235. doi: 10.1107/S2052252518001021. eCollection, 2018 Mar 1. PMID:29765612 doi:http://dx.doi.org/10.1107/S2052252518001021
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