ID K0GV72_9HIV1 Unreviewed; 1003 AA.
AC K0GV72;
DT 28-NOV-2012, integrated into UniProtKB/TrEMBL.
DT 28-NOV-2012, sequence version 1.
DT 27-MAR-2024, entry version 59.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AFU28386.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AFU28386.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AFU28386.1};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AFU28386.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=AA039a01L {ECO:0000313|EMBL:AFU28386.1};
RX PubMed=22960785; DOI=10.1038/nature11519;
RA Rolland M., Edlefsen P.T., Larsen B.B., Tovanabutra S., Sanders-Buell E.,
RA Hertz T., de Camp A.C., Carrico C., Menis S., Magaret C.A., Ahmed H.,
RA Juraska M., Chen L., Konopa P., Nariya S., Stoddard J.N., Wong K., Zhao H.,
RA Deng W., Maust B.S., Bose M., Howell S., Bates A., Lazzaro M.,
RA O'Sullivan A., Lei E., Bradfield A., Ibitamuno G., Assawadarachai V.,
RA O'Connell R.J., de Souza M.S., Nitayaphan S., Rerks-Ngarm S., Robb M.L.,
RA McLellan J.S., Georgiev I., Kwong P.D., Carlson J.M., Michael N.L.,
RA Schief W.R., Gilbert P.B., Mullins J.I., Kim J.H.;
RT "Increased HIV-1 vaccine efficacy against viruses with genetic signatures
RT in Env V2.";
RL Nature 490:417-420(2012).
RN [2] {ECO:0000313|EMBL:AFU28386.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=AA039a01L {ECO:0000313|EMBL:AFU28386.1};
RX PubMed=25646817;
RG RV144 Sequencing Team;
RA Edlefsen P.T., Rolland M., Hertz T., Tovanabutra S., Gartland A.J.,
RA deCamp A.C., Magaret C.A., Ahmed H., Gottardo R., Juraska M., McCoy C.,
RA Larsen B.B., Sanders-Buell E., Carrico C., Menis S., Kijak G.H., Bose M.,
RA Arroyo M.A., O'Connell R.J., Nitayaphan S., Pitisuttithum P.,
RA Kaewkungwal J., Rerks-Ngarm S., Robb M.L., Kirys T., Georgiev I.S.,
RA Kwong P.D., Scheffler K., Pond S.L., Carlson J.M., Michael N.L.,
RA Schief W.R., Mullins J.I., Kim J.H., Gilbert P.B.;
RT "Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144
RT vaccine efficacy trial.";
RL PLoS Comput. Biol. 11:E1003973-E1003973(2015).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3'-end directed exonucleolytic cleavage of viral RNA-DNA
CC hybrid.; EC=3.1.13.2; Evidence={ECO:0000256|ARBA:ARBA00000379};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endohydrolysis of RNA in RNA/DNA hybrids. Three different
CC cleavage modes: 1. sequence-specific internal cleavage of RNA. Human
CC immunodeficiency virus type 1 and Moloney murine leukemia virus
CC enzymes prefer to cleave the RNA strand one nucleotide away from the
CC RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides
CC from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides
CC away from the primer terminus.; EC=3.1.26.13;
CC Evidence={ECO:0000256|ARBA:ARBA00023415};
CC -!- SIMILARITY: Belongs to the retroviral Pol polyprotein family.
CC {ECO:0000256|RuleBase:RU004064}.
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DR EMBL; JX447142; AFU28386.1; -; Genomic_RNA.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004533; F:exoribonuclease H activity; IEA:UniProtKB-EC.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
DR GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
DR CDD; cd05482; HIV_retropepsin_like; 1.
DR CDD; cd01645; RT_Rtv; 1.
DR Gene3D; 1.10.10.200; -; 1.
DR Gene3D; 3.30.70.270; -; 3.
DR Gene3D; 2.40.70.10; Acid Proteases; 1.
DR Gene3D; 3.10.10.10; HIV Type 1 Reverse Transcriptase, subunit A, domain 1; 1.
DR Gene3D; 2.30.30.10; Integrase, C-terminal domain superfamily, retroviral; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 2.
DR InterPro; IPR001969; Aspartic_peptidase_AS.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR017856; Integrase-like_N.
DR InterPro; IPR036862; Integrase_C_dom_sf_retrovir.
DR InterPro; IPR001037; Integrase_C_retrovir.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR003308; Integrase_Zn-bd_dom_N.
DR InterPro; IPR001995; Peptidase_A2_cat.
DR InterPro; IPR021109; Peptidase_aspartic_dom_sf.
DR InterPro; IPR034170; Retropepsin-like_cat_dom.
DR InterPro; IPR018061; Retropepsins.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR002156; RNaseH_domain.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR000477; RT_dom.
DR InterPro; IPR010659; RVT_connect.
DR InterPro; IPR010661; RVT_thumb.
DR PANTHER; PTHR41694; ENDOGENOUS RETROVIRUS GROUP K MEMBER POL PROTEIN; 1.
DR PANTHER; PTHR41694:SF3; RNA-DIRECTED DNA POLYMERASE-RELATED; 1.
DR Pfam; PF00552; IN_DBD_C; 1.
DR Pfam; PF02022; Integrase_Zn; 1.
DR Pfam; PF00075; RNase_H; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF00077; RVP; 1.
DR Pfam; PF00078; RVT_1; 1.
DR Pfam; PF06815; RVT_connect; 1.
DR Pfam; PF06817; RVT_thumb; 1.
DR SUPFAM; SSF50630; Acid proteases; 1.
DR SUPFAM; SSF50122; DNA-binding domain of retroviral integrase; 1.
DR SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR SUPFAM; SSF46919; N-terminal Zn binding domain of HIV integrase; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 2.
DR PROSITE; PS50175; ASP_PROT_RETROV; 1.
DR PROSITE; PS00141; ASP_PROTEASE; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
DR PROSITE; PS51027; INTEGRASE_DBD; 1.
DR PROSITE; PS50879; RNASE_H_1; 1.
DR PROSITE; PS50878; RT_POL; 1.
DR PROSITE; PS50876; ZF_INTEGRASE; 1.
PE 3: Inferred from homology;
KW Aspartyl protease {ECO:0000256|ARBA:ARBA00022750,
KW ECO:0000256|RuleBase:RU004064};
KW DNA integration {ECO:0000256|ARBA:ARBA00022908};
KW DNA recombination {ECO:0000256|ARBA:ARBA00023172};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Endonuclease {ECO:0000256|ARBA:ARBA00022759};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|RuleBase:RU004064};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Protease {ECO:0000256|ARBA:ARBA00022670, ECO:0000256|RuleBase:RU004064};
KW RNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022918};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Viral genome integration {ECO:0000256|ARBA:ARBA00023195};
KW Viral release from host cell {ECO:0000256|ARBA:ARBA00023113};
KW Virion maturation {ECO:0000256|ARBA:ARBA00023113};
KW Virus entry into host cell {ECO:0000256|ARBA:ARBA00023296};
KW Zinc {ECO:0000256|ARBA:ARBA00022833};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771, ECO:0000256|PROSITE-
KW ProRule:PRU00450}.
FT DOMAIN 76..145
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 199..389
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 589..712
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 718..759
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 769..919
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 938..985
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 938..985
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 12..52
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 12..34
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AFU28386.1"
SQ SEQUENCE 1003 AA; 113603 MW; E498AEB9088945C5 CRC64;
FFRENLAFQQ GEARKFSSEQ TRTNSPTSRE PWSGGRDNPL SKAGTRGQGT ISSSSFPQIT
LWQRPIVTVK IGGQLIEALL DTGADDTVLE EINLPGKWKP KMIGGIGGFI KVRQYDQILI
EIDGRKAMGT VLVGPTPVNI IGRNMLTQIG CTLNLPISPI ETVPVKLKPG MDGPKVKQWP
LTEEKIKALT EICAEMEKEG KISKIGPENP YNTPVFAIKK KDSTKWRKLV DFRELNKRTQ
DFWEVQLGIP HPAGLKKKKS ITVLDVGDAY FSVPLDESFR KYTAFTIPSI NNETPGIRYQ
YNVLPQGWKG SPAIFQASMT KILEPFRTKN PEMVIYQYMD DLYVGSDLEI GQHRAKIEEL
REHLLKWGFT TPDKKHQKEP PFLWMGYELH PDKWTVQPIQ LPNKDSWTVN DIQKLVGKLN
WASQIYAGIK VKQLCRLLRG AKALTDIVTL TEEAELELAE NREILKEPVH GVYYDPTKDL
IAEIQKQGQD QWTYQIYQEP FKNLKTGKYA KKRSAHTNDV KQLAEVVQKA ATESIVIWGK
TPKFRLPIQR XTWETWWMEY WQATWIPEWE FVNTPPLVKL WYQLEKDPIV GAETFYVDGA
ANRETKLGKA GYVTDGGRQK VVSLTETTNQ KTELHAIYLA LQDSGSEVNI VTDSQYALGI
IQAQPDRSES ELVNQIIEKL IEKDKIYLSW VPAHKGIGGN EQVDKLVSNG IRKVLFLDGI
DKAQEEHERY HNNWRAMASD FNLPPVVAKE IVACCDKCQL KGEAMHGQVD CRPGIWQLDC
THLEGKIILV AVHVASGYIE AEVIPAETGQ ETAYFILKLA GRWPVKVIHT DNGSNFTSAA
VKAACWWANV TQEFGIPYNP QSQGVVESMN KELKKIIGQV RDQAEHLKTA VQMAVFIHNF
KRKGGIGGYS AGERIIDIIA SDIQTKELQK QITKIQNFRV YYRDSRDPIW KGPAKLLWKG
EGAVVIQDNS DIKVVPRRKA KIIRDYGKQM AGDDCVASRQ DED
//
