ID K0GRC8_9HIV1 Unreviewed; 1003 AA.
AC K0GRC8;
DT 28-NOV-2012, integrated into UniProtKB/TrEMBL.
DT 28-NOV-2012, sequence version 1.
DT 27-MAR-2024, entry version 61.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AFU32388.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AFU32388.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AFU32388.1};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AFU32388.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=AA101a_LH15 {ECO:0000313|EMBL:AFU32388.1};
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:AFU32388.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=AA101a_LH15 {ECO:0000313|EMBL:AFU32388.1};
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; JX447916; AFU32388.1; -; 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..55
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 12..28
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AFU32388.1"
SQ SEQUENCE 1003 AA; 113658 MW; 7FEFA52A2677A962 CRC64;
FFRENLAFQQ GKAREFSSEQ TRANSPTSXE LGDGGRDNLP TEAGTERQGT PSSFSFPQIT
LWQRPLVTVK IGGQLKEALL DTGADDTVLE DINLPGKWKP KMIGGIGGFI KVRQYDQIAI
EICGKKAIGT VLVGPTPVNI IGRNMLTQIG CTLNFPISPI DTIPVTLKPG MDGPKVKQWP
LTEEKIKALT EICTEMEKEG KISKIGPENP YNTPVFAIKK KDSTKWRKLV DFRELNKRTQ
DFWEVQLGIP HPAGLKKKKS VTVLDVGDAY FSVPLDESFR RYTAFTIPSI NNETPGIRYQ
YNVLPQGWKG SPAIFQSSMT KILEPFRIKN PEIIIYQYMD DLYVGSDLEI GQHRIKIEEL
RAHLLSWGFT TPDKKHQKEP PFLWMGYELH PDRWTVQPIE LPEKDSWTVN DIQKLVGKLN
WASQIYAGIK IKQLCKLLRG AKALTDIVPL TEEAELELAE NREXLKNPVH GVYYDPSKDL
VAEVQKQGQD QWTYQIYQEP FKNLKTGKYA RKRSAHTNDV RQLTEVVQKI ATESIVIWGK
TPKFKLPIQK ETWETWWMDY WQATWIPEWE FVNTPPLVKL WYQLEKDPIV GAETFYVDGA
ASRETKLGKA GYVTNRGRQK VVSLTETTNQ KTELHAIYLA LQDSGSEVNI VTDSQYALGI
IQAQPDRSES EIVNQIIEEL IKKEKVYLSW VPAHKGIGGN EQVDKLVSSG IRKVLFLDGI
DKAQEEHERY HSNWRTMASD FNLPPIVAKE IVANCDKCQL KGEAMHGQVD CSPGIWQLDC
THLEGKVILV AVHVASGYIE AEVIPAETGH ETAYFLLKLA GRWPVKVIHT DNGSNFTSAA
VKAACWWANV RQEFGIPYNP QSQGVVESMN KELKKIIGQI REQAEHLKTA VQMAVFIHNF
KRKGGIGEYS AGERIIDIIA TDIQTKELQK QITKIQNFRV YYRDSRDPVW KGPAKLLWKG
EGAVVIQDNS DIKVVPRRKA KIIRDYGKQM AGDDCVAGRQ NED
//
