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{{STRUCTURE_4ol8|  PDB=4ol8  |  SCENE=  }}
===Ty3 reverse transcriptase bound to DNA/RNA===
{{ABSTRACT_PUBMED_24608367}}


==Function==
==Ty3 reverse transcriptase bound to DNA/RNA==
[[http://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> 
<StructureSection load='4ol8' size='340' side='right'caption='[[4ol8]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<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 id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</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 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>
</table>
<div style="background-color:#fffaf0;">
== 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.


==About this Structure==
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>
[[4ol8]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OL8 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<ref group="xtra">PMID:024608367</ref><references group="xtra"/><references/>
</div>
[[Category: Bona, M K.]]
<div class="pdbe-citations 4ol8" style="background-color:#fffaf0;"></div>
[[Category: Grice, S F.J Le.]]
 
[[Category: Jurkowski, J.]]
==See Also==
[[Category: Miller, J T.]]
*[[Reverse transcriptase 3D structures|Reverse transcriptase 3D structures]]
[[Category: Nowak, E.]]
== References ==
[[Category: Nowotny, M.]]
<references/>
[[Category: Studnicka, J.]]
__TOC__
[[Category: Szczepanowski, R H.]]
</StructureSection>
[[Category: Dna/rna binding]]
[[Category: Large Structures]]
[[Category: Hydrolase-rna-dna complex]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Protein-dna/rna]]
[[Category: Bona MK]]
[[Category: Reverse transcription]]
[[Category: Jurkowski J]]
[[Category: Transferase]]
[[Category: Le Grice SFJ]]
[[Category: Miller JT]]
[[Category: Nowak E]]
[[Category: Nowotny M]]
[[Category: Studnicka J]]
[[Category: Szczepanowski RH]]
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