View source for 3oyb


==Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI MK2048==
<StructureSection load='3oyb' size='340' side='right'caption='[[3oyb]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3oyb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Foamv Foamv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OYB 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZZX:(6S)-2-(3-CHLORO-4-FLUOROBENZYL)-8-ETHYL-10-HYDROXY-N,6-DIMETHYL-1,9-DIOXO-1,2,6,7,8,9-HEXAHYDROPYRAZINO[1,2 1,5]PYRROLO[2,3-D]PYRIDAZINE-4-CARBOXAMIDE'>ZZX</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dlr|3dlr]], [[3l2q|3l2q]], [[3l2r|3l2r]], [[3l2u|3l2u]], [[3l2v|3l2v]], [[3l2w|3l2w]], [[3oy9|3oy9]], [[3oya|3oya]], [[3oyc|3oyc]], [[3oyd|3oyd]], [[3oye|3oye]], [[3oyf|3oyf]], [[3oyg|3oyg]], [[3oyh|3oyh]], [[3oyi|3oyi]], [[3oyj|3oyj]], [[3oyk|3oyk]], [[3oyl|3oyl]], [[3oym|3oym]], [[3oyn|3oyn]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 FOAMV])</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=3oyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oyb OCA], [https://pdbe.org/3oyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oyb RCSB], [https://www.ebi.ac.uk/pdbsum/3oyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oyb ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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 in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Lys1,2 binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity).  Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity). 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The development of HIV integrase (IN) strand transfer inhibitors (INSTIs) and our understanding of viral resistance to these molecules have been hampered by a paucity of available structural data. We recently reported cocrystal structures of the prototype foamy virus (PFV) intasome with raltegravir and elvitegravir, establishing the general INSTI binding mode. We now present an expanded set of cocrystal structures containing PFV intasomes complexed with first- and second-generation INSTIs at resolutions of up to 2.5 A. Importantly, the improved resolution allowed us to refine the complete coordination spheres of the catalytic metal cations within the INSTI-bound intasome active site. We show that like the Q148H/G140S and N155H HIV-1 IN variants, the analogous S217H and N224H PFV INs display reduced sensitivity to raltegravir in vitro. Crystal structures of the mutant PFV intasomes in INSTI-free and -bound forms revealed that the amino acid substitutions necessitate considerable conformational rearrangements within the IN active site to accommodate an INSTI, thus explaining their adverse effects on raltegravir antiviral activity. Furthermore, our structures predict physical proximity and an interaction between HIV-1 IN mutant residues His148 and Ser/Ala140, rationalizing the coevolution of Q148H and G140S/A mutations in drug-resistant viral strains.

Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.,Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P Proc Natl Acad Sci U S A. 2010 Oct 28. PMID:21030679<ref>PMID:21030679</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3oyb" style="background-color:#fffaf0;"></div>

==See Also==
*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Foamv]]
[[Category: Large Structures]]
[[Category: Cherepanov, P]]
[[Category: Hare, S]]
[[Category: Dna integration]]
[[Category: Dna-binding]]
[[Category: Dna-binding protein-dna complex]]
[[Category: Endonuclease]]
[[Category: Hhcc motif]]
[[Category: Inhibitor]]
[[Category: Metal-binding]]
[[Category: Multifunctional enzyme]]
[[Category: Nuclease]]
[[Category: Nucleotidyltransferase]]
[[Category: Nucleus]]
[[Category: Protein-dna complex]]
[[Category: Recombination]]
[[Category: Tetramer]]
[[Category: Transferase]]
[[Category: Viral nucleoprotein]]
[[Category: Viral protein]]
[[Category: Viral protein-dna complex]]
[[Category: Virion]]
[[Category: Zinc binding]]