ID D5L1P4_9HIV1 Unreviewed; 1005 AA.
AC D5L1P4;
DT 15-JUN-2010, integrated into UniProtKB/TrEMBL.
DT 15-JUN-2010, sequence version 1.
DT 27-MAR-2024, entry version 78.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:ADE45294.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:ADE45294.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:ADE45294.1, ECO:0000313|Proteomes:UP000142494};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:ADE45294.1, ECO:0000313|Proteomes:UP000142494}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=20519388; DOI=10.1128/JVI.00362-10;
RA Sahu G.K., Sarria J.C., Cloyd M.W.;
RT "Recovery of replication-competent residual HIV-1 from plasma of a patient
RT receiving prolonged, suppressive highly active antiretroviral therapy.";
RL J. Virol. 84:8348-8352(2010).
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; GU733715; ADE45294.1; -; Genomic_DNA.
DR Proteomes; UP000142494; Genome.
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 78..147
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 201..391
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 591..714
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 720..761
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 771..921
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 940..987
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 940..987
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 17..52
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:ADE45294.1"
SQ SEQUENCE 1005 AA; 113949 MW; 30341FA899F658F3 CRC64;
FFRENLAFPQ GKAREFSSEQ TRAISPTSRE LRVWGGGNNS PSEAGDNDSR QGTVSFDLPQ
ITLWQRPLVT IKIGGQLIEA LLDTGADDTV LEDIDLPGRW KPKIIGGIGG FIRVRQYDHV
PIEICGQKAI TTVLIGPTPV NIIGRNLMTQ IGCTLNFPIS PIETVPVKLK PGMDGPRVKQ
WPLTEEKIKA LVEICTELEK EGKISKIGPE NPYNTPVFVI KKKDSTKWRK LTDFRELNKR
TQDFWEVQLG IPHPSGLKKK KSVTVLDVGD AYFSVPLDKD FRKYTAFTIP SINNETPGIR
YQYNVLPQGW KGSPAIFQSS MTKILEPFRK QNPDIVIYQY MDDLYVGSDL EIGQHRTKIE
ELRQHLLKWG FYTPDKKHQK EPPFLWMGYE LHPDKWTVQP IVLPEKDSWT VNDLQKLVGK
LNWASQIYPG IKVKQLCKLL RGTKALTEVV PLTAEAELEL AENREILKEP VHGVYYDPSK
ELIAEIQKQG LGQWTYQIYQ EPFKNLKTGK YARMRGAHTN DVKQLTEAVQ KISTESIVIW
GRTPKFRLPI QKETWETWWT DYWQATWIPE WEFVNTPPLV KLWYQLEKEP IAGAETFYVD
GAANRETKLG RAGYVTDRGR QKVISLTDTT NQKTELQAIH LALQDSGSEV NIVTDSQYAL
GIIQAQPDKS ESELVNQIIE LLINKEKIYL AWVPAHKGIG GNEQVDKLVS AGIRKVLFLD
GIDRAQEDHE KYHSNWRAMA NDFNLPPIVA KEIVASCDKC QVKGEAMHGQ VDCSPGIWQL
DCTHLEGKII LVAVHVASGY IEAEVIPAET GQETAYFILK LAGRWPVKTV HTDNGPNFIS
TAVKAACWWA GIKQEFGIPY NPQSQGVVES MNKELKKIIE QVRDQAEHLK TAVQMAVFIH
NFKRKGGIGG YSAGERIVDI VATDIQTKEL QKQITKIQNF RVYYRDSRDP IWKGPAKLLW
KGEGAVVIQD NSDIKVVPRR KAKIIRDYGK QMAGDDCVAS RQDED
//
