ID M4PDL3_9HIV1 Unreviewed; 993 AA.
AC M4PDL3;
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:AGH00322.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AGH00322.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AGH00322.1};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AGH00322.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=B.700010470.w04.41dps.5_B7 {ECO:0000313|EMBL:AGH00322.1};
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:AGH00322.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=B.700010470.w04.41dps.5_B7 {ECO:0000313|EMBL:AGH00322.1};
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; JX973449; AGH00322.1; -; 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 82..151
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 205..395
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 595..718
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 724..765
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 775..925
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 944..991
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 944..991
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 13..55
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 16..55
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AGH00322.1"
FT NON_TER 993
FT /evidence="ECO:0000313|EMBL:AGH00322.1"
SQ SEQUENCE 993 AA; 112518 MW; 5D5A02BEDC1A3220 CRC64;
FFRENLAFLQ GEARELSSEQ ARTNSPTRAN SPTRSELQIW GGDNNSLSET GDNRQGTVSY
DLPQITLWQR PLVTIKVGGQ LKEALLDTGA DDTVLEEMNL PGRWKPKMIG GIGGFIKVRQ
YDQIAIEICG HKAIGTVLIG PTPVNIIGRN LLTQIGCTLN FPISPIETVP VKLKPGMDGP
KVKQWPLTEE KIKALSEICT EMEKEGKISR IGPENPYNTP IFAIKKKDST KWRKLVDFRE
LNKRTQDFWE VQLGIPHPAG LKKKKSVTVL DVGDAYFSVP LDKEFRKYTA FTIPSTNNET
PGIRYQYNVL PQGWKGSPAI FQASMTKILE PFRKQNPEIV IYQYMDDLYV GSDLEIGQHR
TKVEELRQHL LKWGFTTPDK KHQKEPPFLW MGYELHPDKW TVQPIELPNK DSWTVNDIQK
LVGKLNWASQ IYPGIKVKQL CKLLRGTKAL TEVVPLTEEA ELELAENREI LKEPVHGAYY
DPSKDLIAEI QKQGQGQWTY QIYQEPFKNL KTGKYARMRS AHTNDVKQLT EAVQKIATEG
IVIWGKVPKF RLPIQKETWE AWWMEYWQAT WIPEWEFVNT PPLVKLWYQL EKEPIIGAET
FYVDGAANKE TKLGKAGYVT DRGRQKVVSL TDTTNQKTEL QAIHLALQDS GLEVNIVTDS
QYALGIIQAQ PDKSESELVN QIIEQLIKKE KIYLAWVPAH KGIGGNEQVD KLVSSGIRKV
LFLDGIDKAQ EEHEKYHNNW RAMASDFNLP PVVAKEIVAS CDKCQLKGEA MHGQVDCSPG
IWQLDCTHLE GKIILVAVHV ASGYIEAEVI PAETGQETAY FILKLAGRWP VKTIHTDNGG
NFVSTVVKAA CWWAGIKQEF GIPYNPQSQG VVESMNNELK KIIGQVRDQA EHLKTAVQMA
VFIHNFKRKG GIGGYSAGER IVDIIATDIQ TKELQKQISK IQNFRVYYRD SRDPLWKGPA
KLLWKGEGAV VIQDNSEIKV VPRRKAKIIR DYG
//
