ID M4N7C4_9HIV1 Unreviewed; 1003 AA.
AC M4N7C4;
DT 29-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 29-MAY-2013, sequence version 1.
DT 27-MAR-2024, entry version 58.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AGG76690.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AGG76690.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AGG76690.1};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AGG76690.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=WARO_5_C14 {ECO:0000313|EMBL:AGG76690.1};
RA Parrish N., Li H., Shaw G., Hahn B.;
RL Submitted (DEC-2012) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:AGG76690.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=WARO_5_C14 {ECO:0000313|EMBL:AGG76690.1};
RX PubMed=23542380; DOI=10.1073/pnas.1304288110;
RA Parrish N.F., Gao F., Li H., Giorgi E.E., Barbian H.J., Parrish E.H.,
RA Zajic L., Iyer S.S., Decker J.M., Kumar A., Hora B., Berg A., Cai F.,
RA Hopper J., Denny T.N., Ding H., Ochsenbauer C., Kappes J.C., Galimidi R.P.,
RA West A.P.Jr., Bjorkman P.J., Wilen C.B., Doms R.W., O'Brien M.,
RA Bhardwaj N., Borrow P., Haynes B.F., Muldoon M., Theiler J.P., Korber B.,
RA Shaw G.M., Hahn B.H.;
RT "Phenotypic properties of transmitted founder HIV-1.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:6626-6633(2013).
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; KC312356; AGG76690.1; -; 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 1..41
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..41
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AGG76690.1"
SQ SEQUENCE 1003 AA; 113916 MW; 0546E2402A346973 CRC64;
FFRENLAFPQ GEAREFPSEQ TRANSPTRRE LQVWGRDSNS LSEAGANRQG YVSHDFPQIT
LWQRPLVTIK IGGQLKEALL DTGADDTVLE EMTLPGKWKP KMIGGIGGFI KVRQYDQIPI
EICGHRAMGT VLVGPTPVNI IGRNLLTQIG CTLNFPISPI ETVPVKLKPG MDGPKVKQWP
LTEEKIKALV EICTEMEKEG KISRIGPENP YNTPVFAIKK KDSTKWRKLV DFRELNKKTQ
DFWEVQLGIP HPAGLKKKKS VTVLDVGDAY FSVPLDKDFR KYTAFTIPST NNETPGIRYQ
YNVLPQGWKG SPAIFQSSMT KILEPFRQQN PDIVIYQYMD DLYVGSDLEI GQHRTKIEEL
RQHLLRWGFT TPDKKHQKEP PFLWMGYELH PDKWTVQPIV LPEKDSWTVN DIQKLVGKLN
WASQIYAGIK VRQLCKLLRG TKALTEVIPL TEEAELELAE NREILKEPVH GVYYDPSKDL
IAEIQKQGQG QWTYQIYQEP FKNLKTGKYA RMRGAHTNDV KQLTEAVQKI ATESIVIWGK
IPKFRLPIQK ETWESWWTDY WQATWIPEWE FVNTPPLVKL WYQLEKEPIV GVETFYVDGA
ANRETKLGKA GYVTDRGRQK VVSLTDTTNQ KTELQAIQMA LQDSGLEVNI VTDSQYALGI
IQAQPDKSES AIVNQIIEQL IKKERVYLTW VPAHKGIGGN EQVDKLVSAG IRKVLFLDGI
DKAQEEHEKY HSNWRAMASD FNLPPVVAKE IVACCDKCQQ KGEAMHGQVD CSPGIWQLDC
THLEGKVILV AVHVASGYIE AEVIPAETGQ ETAYFLLKLA GRWPVKTIHT DNGSNFTSTT
VKAACWWAGI KQEFGIPYNP QSQGVVESMN KELKKIIGQV RDQAEHLKTA VQMAVFIHNF
KRKGGIGGYS AGERIVDMIA TDIQTKELQK QITKIQNFRV YYRDSRDPLW KGPAKLLWKG
EGAVVIQDNS DIKVVPRRKA KIIRDYGKQM AGDDCVASRQ DED
//
