ID F1K6C7_9HIV1 Unreviewed; 1003 AA.
AC F1K6C7;
DT 03-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 03-MAY-2011, sequence version 1.
DT 27-MAR-2024, entry version 70.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:ADZ34327.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:ADZ34327.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:ADZ34327.1};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:ADZ34327.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=502-2696_LH03 {ECO:0000313|EMBL:ADZ34327.1};
RX PubMed=21358627;
RA Rolland M., Tovanabutra S., deCamp A.C., Frahm N., Gilbert P.B.,
RA Sanders-Buell E., Heath L., Magaret C.A., Bose M., Bradfield A.,
RA O'Sullivan A., Crossler J., Jones T., Nau M., Wong K., Zhao H., Raugi D.N.,
RA Sorensen S., Stoddard J.N., Maust B.S., Deng W., Hural J., Dubey S.,
RA Michael N.L., Shiver J., Corey L., Li F., Self S.G., Kim J., Buchbinder S.,
RA Casimiro D.R., Robertson M.N., Duerr A., McElrath M.J., McCutchan F.E.,
RA Mullins J.I.;
RT "Genetic impact of vaccination on breakthrough HIV-1 sequences from the
RT STEP trial.";
RL Nat. Med. 17:366-371(2011).
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; JF320306; ADZ34327.1; -; 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 10..38
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 11..31
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:ADZ34327.1"
SQ SEQUENCE 1003 AA; 113774 MW; 25CDBDB26ECDC241 CRC64;
FFRENLAFQQ REARKLSSEQ TRTNSPTSRE LWDGGRGNLL SEAGTEGQRA ISSLNLPQIT
LWQRPLVTAK IGEQLIEALL DTGADDTVLE DINLPGKWKP KMIGGIGGFI KVRQYDQILI
EICGKKAVGT VLVGPTPVNI IGRNMLTQIG CTLNFPISPI ETVPVKLKPG MDGPKVKQWP
LTEEKIKALT EICTEMEREG KISKIGPENP YNTPIFAIKK KDGTKWRKLV DFRELNKRTQ
DFWEVQLGIP HPAGLKKKKS VTVLDVGDAY FSVPLDKDFR KYTAFTIPSI NNETPGIRYQ
YNVLPQGWKG SPAIFQASMT KILEPFRAKN PEMVIYQYMD DLYVGSDLEI GQHRTKIQEL
REHLLKWGLT TPDKKHQKEP PFLWMGYELH PDKWTVQPIK LPEKDSWTVN DIQKLVGKLN
WASQIYAGIK VRQLCKLLRG AKALTEIVTL TEEAELELAE NREILKEPVH GVYYDPSKDL
VAEIQKQGQD QWTYQIYQEP FKNLKTGKYA KKKSAHTNDV KQLTEVVQRV STESIVIWGK
TPKFRLPIQK ETWEAWWREY WQATWIPEWE FVNTPPLVKL WYQLEKDPIV GAETFYVDGA
ANRETKLGKA GYVTDRGRQK VVPLTETTNQ KTELHAIHLA LQDSGSEVNI VTDSQYALGI
IQAQPDRSES ELVNQIIEKL IEKDKVYLSW VPAHKGIGGN EQVDKLVSSG IRKVLFLDGI
DKAQEEHERY HSNWRAMASD FNLPPIVAKE IVASCDKCQL KGEAMHGQVD CSPGIWQLDC
THLEGKIILV AVHVASGYIE AEVIPAETGQ ETAYFILKLA GRWPVKVIHT DNGSNFTSAA
VKAACWWANV TQEFGIPYNP QSQGVVESMN KQLKQIIGQV RDQAEHLKTA VQMAVFIHNF
KRKGGIGGYS AGERIIDMIA SDLQTKELQK QIIKIQNFRV YYRDSRDPIW KGPAKLLWKG
EGAVVIQDNS DIKVVPRRKV KIIRDYGKQM AGDDCVAGRQ DEN
//
