Protein: POL_HV2CA
Sequence: MGARNSVLRGKKADELEKVRLRPGGKKKYKLKHIVWAANELDRFGLAESLLESKEGCQRILKVLDPLVPTGSENLKSLFNTVCVIWCIHAEEKVKDTEEAKRIALRHLAAETGTAEKMPDTSRPTAPPSGKGGNYPVQSIGGNYTHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAADWDANHPIPGPLPAGQLRDPRGSDIAGTTSTVEEQIQWMFRAQNPVPVGNIYRRWIQIGLQKCVRMYNPTNILDIKQGPKESFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLVQNANPDCKLVLKGLGMNPTLEEMLTACQGVGGPGQKARLMAEALKEAMGPPPIPFAAAQQRRTIKCWNCGKEGHSARQCRAPRRQGCWKCGKPGHIMTNCPDRQAGFLRDWPLGKEAPQFPRGPSSTGANTNSTPIGSSSGSTGEIYAAREKAEGAETETIQRGDRGLTAPRTRRGPMQGDNRGLAAPQFSLWKRPVVTAHIEGQPVEVLLDTGADDSIVAGIELGSNYSPKIVGGIGGFINTKEYKNVEIEVLGKRVRATIMTGDTPINIFGRNILTALGMSLNLPVAKIEPIKIMLKPGKDGPRLRQWPLTKEKIEALKEICEKMEKEGQLEEAPPTNPYNTPTFAIRKKDKNKWRMLIDFRELNKVTQDFTEIQLGIPHPAGLAKKRRITVLDVGDAYFSIPLHEDFRQYTAFTLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQYTMRQVLEPFRKANSDVIIIQYMDDILIASDRTDLEHDKVVLQLKELLNNLGFSTPDEKFQKDPPYRWMGYELWPTKWKLQKIQLPQKEVWTVNDIQKLVGVLNWAAQIYPGIKTKHLCRLIRGKMTLTEEVQWTELAEAELEENRIILSQEQEGHYYQEEKELEATVQKDQDNQWTYKIHQEEKILKVGKYAKIKHTHTNGVKLLAQVVQKIGKEALVIGRIPKFHLPVEREVWEQWWDNYWQVTWIPDWDFVSTPPLVRLAFNLVGDPIPGTETFYTDGSCNRQSKEGKAGYVTDRGRDKVKILEQTTNQQAELEAFAMALTDSGPKANIIVDSQYVMGIVAGQPTESENRIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGIRQVLFLEKIEPAQEEHEKYHTNVKELCHKFDIPQLVARQIVNTCAQYQQKGEAIHGQVNAEVGTWQMDCTHLEGKIIIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRWPITHLHTDNGANFTSQEVKMVAWWVGIEQTFGVPYNPQSQGVVEAMNHHLKNQISRIREQANTVETIVLMAVHCMNFKRRGGIGDMTPSERLINMITTEQEIQFLQAKNSKLKNFRVYFREGRDQLWKGPGELLWKGDGAVIVKVGTDIKIIPRRKAKIIRDYGGRQELDSSSHLEGARENGEVA
What is the function of this protein?
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 the viral genome, matrix protein, Vpr and integrase.  This complex is called the pre-integration complex (PIC).  The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends.  In the second step, the PIC enters cell nucleus.  This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell.  This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes.  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.  The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart.  A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp.  The last step is viral DNA integration into host chromosome.  This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated.  Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration.  Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.
What are the official names of this protein?
Gag-Pol polyprotein, Pr160Gag-Pol.
What are the subcellular locations of this protein?
[Gag-Pol polyprotein]: Host cell membrane; Lipid- anchor. Host endosome, host multivesicular body. Note=These locations are linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly. SUBCELLULAR LOCATION: [Matrix protein p17]: Virion membrane; Lipid- anchor. Host nucleus. Host cytoplasm. SUBCELLULAR LOCATION: [Capsid protein p24]: Virion. SUBCELLULAR LOCATION: [Nucleocapsid protein p7]: Virion. SUBCELLULAR LOCATION: [Reverse transcriptase/ribonuclease H]: Virion. SUBCELLULAR LOCATION: [Integrase]: Virion. Host nucleus. Host cytoplasm. Note=Nuclear at initial phase, cytoplasmic at assembly.