ID M4PBD8_9HIV1 Unreviewed; 981 AA.
AC M4PBD8;
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:AGH00778.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AGH00778.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AGH00778.1};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AGH00778.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=C.703010159.w04.29dps.gp8 {ECO:0000313|EMBL:AGH00778.1};
RA Liu M., Hawkins N., Ritchie A., Ganusov V., Whale V., Brackenridge S.,
RA Li H., Pavliceck J., Cai F., Abrahams M.-R., Treurnicht F., Hraber P.,
RA Riou C., Gray C., Ferrari G., Tanner R., Ping L.-H., Anderson J.,
RA Swanstrom R., Cohen M., Abdool Karim S., Haynes B., Borrow P., Perelson A.,
RA Shaw G., Hahn B., Williamson C., Korber B., Gao F., Self S., McMichael A.,
RA Goonetilleke N.;
RL Submitted (OCT-2012) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:AGH00778.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=C.703010159.w04.29dps.gp8 {ECO:0000313|EMBL:AGH00778.1};
RX PubMed=23221345; DOI=10.1172/JCI65330;
RG CHAVI Core B;
RA Liu M.K., Hawkins N., Ritchie A.J., Ganusov V.V., Whale V.,
RA Brackenridge S., Li H., Pavlicek J.W., Cai F., Rose-Abrahams M.,
RA Treurnicht F., Hraber P., Riou C., Gray C., Ferrari G., Tanner R.,
RA Ping L.H., Anderson J.A., Swanstrom R., B C.C., Cohen M., Karim S.S.,
RA Haynes B., Borrow P., Perelson A.S., Shaw G.M., Hahn B.H., Williamson C.,
RA Korber B.T., Gao F., Self S., McMichael A., Goonetilleke N.;
RT "Vertical T cell immunodominance and epitope entropy determine HIV-1
RT escape.";
RL J. Clin. Invest. 123:380-393(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; JX973684; AGH00778.1; -; 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 72..141
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 195..385
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 585..708
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 714..755
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 765..915
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 934..981
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 934..981
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 1..48
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..48
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AGH00778.1"
FT NON_TER 981
FT /evidence="ECO:0000313|EMBL:AGH00778.1"
SQ SEQUENCE 981 AA; 111286 MW; 80646BB4EFF3CFD2 CRC64;
FFRENLAFPQ GKAREFPSEQ TRANSPTSRE LQVRRNNPSS EAGTERQGTL NFPQITLWQR
PLVSIKVGGQ IKEALLDTGA DDTVLEDINL PGKWKPRMIG GIGGFIKVRQ YEQIPIEICG
KKAIGTVLVG PTPVNIIGRN MLTQLGCTLN FPISPIETVP VKLKPGMDGP RVKQWPLTEE
KIKALTAICE EMEKEGKITK IGPENPYNTP IFAIKKKDST KWRKLVDFRE LNKRTQDFWE
VQLGIPHPAG LKKKKSVTVL DVGDAYFSVP LDESFRKYTA FTIPSINNAT PGIRYQYNVL
PQGWKGSPAI FQSSMTKILE PFRTQNPDIV IYQYMDDLYV GSDLEIGQHR AKIEQLREHL
LQWGLTTPDK KHQKEPPFLW MGYELHPDKW TVQPIQLPDK DSWTVNDIQK LVGKLNWASQ
IYPGIKVRQL CKLLRGTKAL TDIVPLTEEA ELELAENREI LKEPVHGVYY DPSKDLIAEI
QKQGHDQWTY QIYQEPFKNL KTGKYAKMRT AHTNDVKQLT EAVQKIAQEC IVIWGKTPKF
RLPIQKDIWE TWWTDYWQAT WIPEWEFSNT PPLVKLWYQL EKDPIAGAET FYVDGAANRE
TKLGKAGYVT DKGRQKIITL TETTNQKAEL QAIQLALQDS GSEVNIVTDS QYALGIIQAQ
PDKSESELVT QIIEQLIGKE RIYLSWVPAH KGIGGNEQVD KLVSSGIRKV LFLDGIDKAQ
EEHEKYHSNW RAMASEFNLP PIVAKEIVAS CDKCQQKGEA MHGQVDCSPG IWQLDCTHLE
GKIILVAVHV ASGYIEAEVI PAETGQETAY YILKLAGRWP VKVIHTDNGS NFTSNAVKAA
CWWAGIQQEF GIPYNPQSQG VVESMNKELK KIIGQVRDQA EHLKTAVQMA VFIHNFKRKG
GIGGYSAGER IIDMIATDIQ TKELQKQIIK IQNFRVYYRD SRDPIWKGPA KLLWKGEGAV
VIQDNSDIKV VPRRKAKIIK D
//
