ID H6CX34_9HIV1 Unreviewed; 994 AA.
AC H6CX34;
DT 18-APR-2012, integrated into UniProtKB/TrEMBL.
DT 18-APR-2012, sequence version 1.
DT 27-MAR-2024, entry version 62.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AFB37763.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AFB37763.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AFB37763.1, ECO:0000313|Proteomes:UP000173967};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AFB37763.1, ECO:0000313|Proteomes:UP000173967}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=USPI71101EI68y04071pcWG2B8 {ECO:0000313|EMBL:AFB37763.1};
RX PubMed=21593162; DOI=10.1128/JVI.02697-10;
RA Herbeck J.T., Rolland M., Liu Y., McLaughlin S., McNevin J., Zhao H.,
RA Wong K., Stoddard J.N., Raugi D., Sorensen S., Genowati I., Birditt B.,
RA McKay A., Diem K., Maust B.S., Deng W., Collier A.C., Stekler J.D.,
RA McElrath M.J., Mullins J.I.;
RT "Demographic processes affect HIV-1 evolution in primary infection before
RT the onset of selective processes.";
RL J. Virol. 85:7523-7534(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; JN024253; AFB37763.1; -; Genomic_RNA.
DR Proteomes; UP000173967; 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 67..136
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 190..380
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 580..703
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 709..750
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 760..910
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 929..976
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 929..976
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 1..38
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 7..38
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AFB37763.1"
SQ SEQUENCE 994 AA; 112491 MW; 04C43AD7DFE75F1D CRC64;
FFREFSSEQD RANSPTRGEL QVWGRDNNSL SEAGTGTDRQ GTVSFNFPQI TLWQRPLVTI
KIGGQLKEAL LDTGADDTVL EDMNLPGRWK PKMIGGIGGF IKVRQYDQVP IEICGHKAIG
TVLVGPTPVN IIGRNLLTQL GCTLNFPISP IETVPVKLKP GMDGPKVKQW PLTEEKIEAL
VEICTEMEKE GKISKIGPEN PYNTPVFAIK KKDSTKWRKL VDFRELNKRT QDFWEVQLGI
PHPAGLKKKK SVTVLDVGDA YFSVPLDKDF RKYTAFTIPS INNETPGIRY QYNVLPQGWK
GSPAIFQSSM TKILDPFRKQ NPDIVIYQYM DDLYVGSDLE IGQHRTKIEE LRQHLLRWGL
TTPDKKHQKE PPFLWMGYEL HPDKWTVQPI VLPEKDSWTV NDIQKLVGKL NWASQIYPGI
KVRQLCKLLR GTKALTEVIT LTEEAELELA ENREILKEPV HGVYYDPSKE LIAELQKQGQ
SQWTYQIYQE PFKNLKTGKY AKVRGAHTND VKQLTEAVQK ITLESIVIWG KTPKFKLPIQ
KETWETWWTE YWQATWIPEW EFVNTPPLVK LWYQLEKEPI VGAETFYVDG AANRESKLGK
AGYVTDRGRQ KVVPLADTTN QKTELQAIHL ALQDSGLEVN IVTDSQYALG IIQAQPDKSE
SELVSQIIEQ LIKKEKVYLA WVPAHKGIGG NEKVDKLVST GIRRVLFLDG IEKAQDDHEK
YHSNWKAMAS DFNLPPVVAK EIVASCDKCQ LKGEAIHGQV DCSPGIWQLD CTHLEGKIII
VAVHVASGYI EAEVIPAETG QETAYFLLKL AGRWPVTTIH TDNGPNFTSA TVKAACWWAG
IKQEFGIPYN PQSQGVVESM NKELKKIIGQ VRDQAEHLKT AVQMAVFIHN FKRKGGIGGY
SAGERIVDII ASDLQTKALQ KQITKIQNFR VYYRDNKDPL WKGPAKLLWK GEGAVVIQDN
SDIKVVPRRK AKIIRDYGKQ MAGDDCVASR QDED
//
