Function of HIV Pol

  • HIV pol gene encodes three viral enzymes: protease, reverse transcriptase and integrase.

  • HIV pol gene is transcripted in Gagpol mRNA during the viral transcription.

  • Most anti-HIV drugs have been developed to target viral enzymes encoded by pol.

Reference

  1. Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne-Mieke Vandamme, Kristof Theys. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology 12, 18, doi:10.1186/s12977-015-0148-6 (2015). [PDF] [PubMed Link]
  2. Guangdi Li, HIV genome-wide diversity, interaction and coevolution. Phd thesis, Faculty of Medicine, KU Leuven, 2014 [KULeuven Link]

Sequence

(1) Reference sequence for HIV-1 Pol

  • Strain: HIV-1 subtype B HXB2 (ID: K03455)

  • Fasta format: Download

  • Reference sequence: 

  1       10         20         30         40         50
  |        |          |          |          |          | 
  FFREDLAFLQ GKAREFSSEQ TRANSPTRRE LQVWGRDNNS PSEAGADRQG 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  TVSFNFPQVT LWQRPLVTIK IGGQLKEALL DTGADDTVLE EMSLPGRWKP 
  101    110        120        130        140        150
  |        |          |          |          |          | 
  KMIGGIGGFI KVRQYDQILI EICGHKAIGT VLVGPTPVNI IGRNLLTQIG 
  151    160        170        180        190        200
  |        |          |          |          |          | 
  CTLNFPISPI ETVPVKLKPG MDGPKVKQWP LTEEKIKALV EICTEMEKEG 
  201    210        220        230        240        250
  |        |          |          |          |          | 
  KISKIGPENP YNTPVFAIKK KDSTKWRKLV DFRELNKRTQ DFWEVQLGIP 
  251    260        270        280        290        300
  |        |          |          |          |          | 
  HPAGLKKKKS VTVLDVGDAY FSVPLDEDFR KYTAFTIPSI NNETPGIRYQ 
  301    310        320        330        340        350
  |        |          |          |          |          | 
  YNVLPQGWKG SPAIFQSSMT KILEPFRKQN PDIVIYQYMD DLYVGSDLEI 
  351    360        370        380        390        400
  |        |          |          |          |          | 
  GQHRTKIEEL RQHLLRWGLT TPDKKHQKEP PFLWMGYELH PDKWTVQPIV 
  401    410        420        430        440        450
  |        |          |          |          |          | 
  LPEKDSWTVN DIQKLVGKLN WASQIYPGIK VRQLCKLLRG TKALTEVIPL 
  451    460        470        480        490        500
  |        |          |          |          |          | 
  TEEAELELAE NREILKEPVH GVYYDPSKDL IAEIQKQGQG QWTYQIYQEP 
  501    510        520        530        540        550
  |        |          |          |          |          | 
  FKNLKTGKYA RMRGAHTNDV KQLTEAVQKI TTESIVIWGK TPKFKLPIQK 
  551    560        570        580        590        600
  |        |          |          |          |          | 
  ETWETWWTEY WQATWIPEWE FVNTPPLVKL WYQLEKEPIV GAETFYVDGA 
  601    610        620        630        640        650
  |        |          |          |          |          | 
  ANRETKLGKA GYVTNRGRQK VVTLTDTTNQ KTELQAIYLA LQDSGLEVNI 
  651    660        670        680        690        700
  |        |          |          |          |          | 
  VTDSQYALGI IQAQPDQSES ELVNQIIEQL IKKEKVYLAW VPAHKGIGGN 
  701    710        720        730        740        750
  |        |          |          |          |          | 
  EQVDKLVSAG IRKVLFLDGI DKAQDEHEKY HSNWRAMASD FNLPPVVAKE 
  751    760        770        780        790        800
  |        |          |          |          |          | 
  IVASCDKCQL KGEAMHGQVD CSPGIWQLDC THLEGKVILV AVHVASGYIE 
  801    810        820        830        840        850
  |        |          |          |          |          | 
  AEVIPAETGQ ETAYFLLKLA GRWPVKTIHT DNGSNFTGAT VRAACWWAGI 
  851    860        870        880        890        900
  |        |          |          |          |          | 
  KQEFGIPYNP QSQGVVESMN KELKKIIGQV RDQAEHLKTA VQMAVFIHNF 
  901    910        920        930        940        950
  |        |          |          |          |          | 
  KRKGGIGGYS AGERIVDIIA TDIQTKELQK QITKIQNFRV YYRDSRNPLW 
  951    960        970        980        990        1000
  |        |          |          |          |          | 
  KGPAKLLWKG EGAVVIQDNS DIKVVPRRKA KIIRDYGKQM AGDDCVASRQ 
  1001
  |
  DED

(2) Reference sequence for HIV-2 and SIV Pol

  • Strain: SIV Mac239 (ID: M33262)

  • Fasta format: Download

  • Reference sequence: 

  1       10         20         30         40         50
  |        |          |          |          |          | 
  PQFSLWRRPV VTAHIEGQPV EVLLDTGADD SIVTGIELGP HYTPKIVGGI 
  51      60         70         80         90         100
  |        |          |          |          |          | 
  GGFINTKEYK NVEIEVLGKR IKGTIMTGDT PINIFGRNLL TALGMSLNFP 
  101    110        120        130        140        150
  |        |          |          |          |          | 
  IAKVEPVKVA LKPGKDGPKL KQWPLSKEKI VALREICEKM EKDGQLEEAP 
  151    160        170        180        190        200
  |        |          |          |          |          | 
  PTNPYNTPTF AIKKKDKNKW RMLIDFRELN RVTQDFTEVQ LGIPHPAGLA 
  201    210        220        230        240        250
  |        |          |          |          |          | 
  KRKRITVLDI GDAYFSIPLD EEFRQYTAFT LPSVNNAEPG KRYIYKVLPQ 
  251    260        270        280        290        300
  |        |          |          |          |          | 
  GWKGSPAIFQ YTMRHVLEPF RKANPDVTLV QYMDDILIAS DRTDLEHDRV 
  301    310        320        330        340        350
  |        |          |          |          |          | 
  VLQSKELLNS IGFSTPEEKF QKDPPFQWMG YELWPTKWKL QKIELPQRET 
  351    360        370        380        390        400
  |        |          |          |          |          | 
  WTVNDIQKLV GVLNWAAQIY PGIKTKHLCR LIRGKMTLTE EVQWTEMAEA 
  401    410        420        430        440        450
  |        |          |          |          |          | 
  EYEENKIILS QEQEGCYYQE GKPLEATVIK SQDNQWSYKI HQEDKILKVG 
  451    460        470        480        490        500
  |        |          |          |          |          | 
  KFAKIKNTHT NGVRLLAHVI QKIGKEAIVI WGQVPKFHLP VEKDVWEQWW 
  501    510        520        530        540        550
  |        |          |          |          |          | 
  TDYWQVTWIP EWDFISTPPL VRLVFNLVKD PIEGEETYYT DGSCNKQSKE 
  551    560        570        580        590        600
  |        |          |          |          |          | 
  GKAGYITDRG KDKVKVLEQT TNQQAELEAF LMALTDSGPK ANIIVDSQYV 
  601    610        620        630        640        650
  |        |          |          |          |          | 
  MGIITGCPTE SESRLVNQII EEMIKKSEIY VAWVPAHKGI GGNQEIDHLV 
  651    660        670        680        690        700
  |        |          |          |          |          | 
  SQGIRQVLFL EKIEPAQEEH DKYHSNVKEL VFKFGLPRIV ARQIVDTCDK 
  701    710        720        730        740        750
  |        |          |          |          |          | 
  CHQKGEAIHG QANSDLGTWQ MDCTHLEGKI IIVAVHVASG FIEAEVIPQE 
  751    760        770        780        790        800
  |        |          |          |          |          | 
  TGRQTALFLL KLAGRWPITH LHTDNGANFA SQEVKMVAWW AGIEHTFGVP 
  801    810        820        830        840        850
  |        |          |          |          |          | 
  YNPQSQGVVE AMNHHLKNQI DRIREQANSV ETIVLMAVHC MNFKRRGGIG 
  851    860        870        880        890        900
  |        |          |          |          |          | 
  DMTPAERLIN MITTEQEIQF QQSKNSKFKN FRVYYREGRD QLWKGPGELL 
  901    910        920        930        940        950
  |        |          |          |          |          | 
  WKGEGAVILK VGTDIKVVPR RKAKIIKDYG GGKEVDSSSH MEDTGEAREV 
  951
  |
  A

(3) Coloring scheme for above amino acids

  1. Amino acids with hydrophobic side chains (normally buried inside the protein core):

    • A - Ala - Alanine

    • I - Ile - Isoleucine

    • L - Leu - Leucine

    • M - Met - Methionine

    • V - Val - Valine

  2. Amino acids with polar uncharged side chains (may participate in hydrogen bonds):

    • N - Asn - Asparagine

    • Q - Gln - Glutamine

    • S - Ser - Serine

    • T - Thr - Threonine

  3. Amino acids with positive charged side chains:

    • H - His - Histidine

    • K - Lys - Lysine

    • R - Arg - Arginine

  4. Amino acids with negative charged side chains:

    • D - Asp - Aspartic acid

    • E - Glu - Glutamic acid

  5. Amino acids with aromatic side chains:

    • F - Phe - Phenylalanine

    • Y - Tyr - Tyrosine

    • W - Trp - Tryptophan

  6. Cysteine: C - Cys - Cysteine

  7. Glycine: G - Gly - Glycine

  8. Proline: P - Pro - Proline

Localization

(1) Coding region of Pol at the HIV genome


(2) Localization of Pol during the HIV-1 life cycle

Here, we visualize the localization of Pol during the viral life cycle. Red stars indicate the appearance of HIV-1 Pol.


Anti-HIV inhibitor

(1) Drug binding pocket of HIV-1 Pol

Here, we visualize the drug binding pocket of HIV-1 Pol



(2) List of known inhibitors targeting HIV-1 Pol

Here, we summarize the published anti-HIV inhibitors which bind to HIV-1 Pol.



Protein-protein interactions