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| | ==Ty3 reverse transcriptase bound to DNA/RNA== | | ==Ty3 reverse transcriptase bound to DNA/RNA== |
| - | <StructureSection load='4ol8' size='340' side='right' caption='[[4ol8]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='4ol8' size='340' side='right'caption='[[4ol8]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ol8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OL8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ol8]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OL8 FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ol8 OCA], [https://pdbe.org/4ol8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ol8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ol8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ol8 ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TY3B-G, YGRWTy3-1 POL, YGR109W-B, G5984 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr> | + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ol8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ol8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ol8 PDBsum]</span></td></tr>
| + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/YG31B_YEAST YG31B_YEAST] Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the genomic RNA-nucleocapsid complex.<ref>PMID:2159534</ref> <ref>PMID:1371165</ref> <ref>PMID:7515969</ref> <ref>PMID:10593967</ref> Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers (By similarity). Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 RNA and initiation of reverse transcription.<ref>PMID:2159534</ref> <ref>PMID:1371165</ref> <ref>PMID:7515969</ref> <ref>PMID:10593967</ref> The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.<ref>PMID:2159534</ref> <ref>PMID:1371165</ref> <ref>PMID:7515969</ref> <ref>PMID:10593967</ref> Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends.<ref>PMID:2159534</ref> <ref>PMID:1371165</ref> <ref>PMID:7515969</ref> <ref>PMID:10593967</ref> Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome.<ref>PMID:2159534</ref> <ref>PMID:1371165</ref> <ref>PMID:7515969</ref> <ref>PMID:10593967</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.,Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SF, Nowotny M Nat Struct Mol Biol. 2014 Mar 9. doi: 10.1038/nsmb.2785. PMID:24608367<ref>PMID:24608367</ref> | | Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.,Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SF, Nowotny M Nat Struct Mol Biol. 2014 Mar 9. doi: 10.1038/nsmb.2785. PMID:24608367<ref>PMID:24608367</ref> |
| | | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4ol8" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Reverse transcriptase 3D structures|Reverse transcriptase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | + | [[Category: Large Structures]] |
| - | [[Category: Bona, M K.]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Grice, S F.J Le.]] | + | [[Category: Bona MK]] |
| - | [[Category: Jurkowski, J.]] | + | [[Category: Jurkowski J]] |
| - | [[Category: Miller, J T.]] | + | [[Category: Le Grice SFJ]] |
| - | [[Category: Nowak, E.]] | + | [[Category: Miller JT]] |
| - | [[Category: Nowotny, M.]] | + | [[Category: Nowak E]] |
| - | [[Category: Studnicka, J.]] | + | [[Category: Nowotny M]] |
| - | [[Category: Szczepanowski, R H.]] | + | [[Category: Studnicka J]] |
| - | [[Category: Dna/rna binding]]
| + | [[Category: Szczepanowski RH]] |
| - | [[Category: Hydrolase-rna-dna complex]]
| + | |
| - | [[Category: Protein-dna/rna]]
| + | |
| - | [[Category: Reverse transcription]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
YG31B_YEAST Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the genomic RNA-nucleocapsid complex.[1] [2] [3] [4] Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers (By similarity). Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 RNA and initiation of reverse transcription.[5] [6] [7] [8] The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.[9] [10] [11] [12] Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends.[13] [14] [15] [16] Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome.[17] [18] [19] [20]
Publication Abstract from PubMed
Retrotransposons are a class of mobile genetic elements that replicate by converting their single-stranded RNA intermediate to double-stranded DNA through the combined DNA polymerase and ribonuclease H (RNase H) activities of the element-encoded reverse transcriptase (RT). Although a wealth of structural information is available for lentiviral and gammaretroviral RTs, equivalent studies on counterpart enzymes of long terminal repeat (LTR)-containing retrotransposons, from which they are evolutionarily derived, is lacking. In this study, we report the first crystal structure of a complex of RT from the Saccharomyces cerevisiae LTR retrotransposon Ty3 in the presence of its polypurine tract-containing RNA-DNA hybrid. In contrast to its retroviral counterparts, Ty3 RT adopts an asymmetric homodimeric architecture whose assembly is substrate dependent. Moreover, our structure and biochemical data suggest that the RNase H and DNA polymerase activities are contributed by individual subunits of the homodimer.
Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.,Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SF, Nowotny M Nat Struct Mol Biol. 2014 Mar 9. doi: 10.1038/nsmb.2785. PMID:24608367[21]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hansen LJ, Sandmeyer SB. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J Virol. 1990 Jun;64(6):2599-607. PMID:2159534
- ↑ Hansen LJ, Chalker DL, Orlinsky KJ, Sandmeyer SB. Ty3 GAG3 and POL3 genes encode the components of intracellular particles. J Virol. 1992 Mar;66(3):1414-24. PMID:1371165
- ↑ Orlinsky KJ, Sandmeyer SB. The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins. J Virol. 1994 Jul;68(7):4152-66. PMID:7515969
- ↑ Cristofari G, Gabus C, Ficheux D, Bona M, Le Grice SF, Darlix JL. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro. J Biol Chem. 1999 Dec 17;274(51):36643-8. PMID:10593967
- ↑ Hansen LJ, Sandmeyer SB. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J Virol. 1990 Jun;64(6):2599-607. PMID:2159534
- ↑ Hansen LJ, Chalker DL, Orlinsky KJ, Sandmeyer SB. Ty3 GAG3 and POL3 genes encode the components of intracellular particles. J Virol. 1992 Mar;66(3):1414-24. PMID:1371165
- ↑ Orlinsky KJ, Sandmeyer SB. The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins. J Virol. 1994 Jul;68(7):4152-66. PMID:7515969
- ↑ Cristofari G, Gabus C, Ficheux D, Bona M, Le Grice SF, Darlix JL. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro. J Biol Chem. 1999 Dec 17;274(51):36643-8. PMID:10593967
- ↑ Hansen LJ, Sandmeyer SB. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J Virol. 1990 Jun;64(6):2599-607. PMID:2159534
- ↑ Hansen LJ, Chalker DL, Orlinsky KJ, Sandmeyer SB. Ty3 GAG3 and POL3 genes encode the components of intracellular particles. J Virol. 1992 Mar;66(3):1414-24. PMID:1371165
- ↑ Orlinsky KJ, Sandmeyer SB. The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins. J Virol. 1994 Jul;68(7):4152-66. PMID:7515969
- ↑ Cristofari G, Gabus C, Ficheux D, Bona M, Le Grice SF, Darlix JL. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro. J Biol Chem. 1999 Dec 17;274(51):36643-8. PMID:10593967
- ↑ Hansen LJ, Sandmeyer SB. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J Virol. 1990 Jun;64(6):2599-607. PMID:2159534
- ↑ Hansen LJ, Chalker DL, Orlinsky KJ, Sandmeyer SB. Ty3 GAG3 and POL3 genes encode the components of intracellular particles. J Virol. 1992 Mar;66(3):1414-24. PMID:1371165
- ↑ Orlinsky KJ, Sandmeyer SB. The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins. J Virol. 1994 Jul;68(7):4152-66. PMID:7515969
- ↑ Cristofari G, Gabus C, Ficheux D, Bona M, Le Grice SF, Darlix JL. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro. J Biol Chem. 1999 Dec 17;274(51):36643-8. PMID:10593967
- ↑ Hansen LJ, Sandmeyer SB. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J Virol. 1990 Jun;64(6):2599-607. PMID:2159534
- ↑ Hansen LJ, Chalker DL, Orlinsky KJ, Sandmeyer SB. Ty3 GAG3 and POL3 genes encode the components of intracellular particles. J Virol. 1992 Mar;66(3):1414-24. PMID:1371165
- ↑ Orlinsky KJ, Sandmeyer SB. The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins. J Virol. 1994 Jul;68(7):4152-66. PMID:7515969
- ↑ Cristofari G, Gabus C, Ficheux D, Bona M, Le Grice SF, Darlix JL. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro. J Biol Chem. 1999 Dec 17;274(51):36643-8. PMID:10593967
- ↑ Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SF, Nowotny M. Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry. Nat Struct Mol Biol. 2014 Mar 9. doi: 10.1038/nsmb.2785. PMID:24608367 doi:http://dx.doi.org/10.1038/nsmb.2785
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