ID F5CFY2_9HIV1 Unreviewed; 1001 AA.
AC F5CFY2;
DT 28-JUN-2011, integrated into UniProtKB/TrEMBL.
DT 28-JUN-2011, sequence version 1.
DT 27-MAR-2024, entry version 68.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AEB52792.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AEB52792.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AEB52792.1, ECO:0000313|Proteomes:UP000120630};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AEB52792.1, ECO:0000313|Proteomes:UP000120630}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CY232 {ECO:0000313|EMBL:AEB52792.1};
RX PubMed=21453134; DOI=10.1089/aid.2011.0060;
RA Kousiappa I., Achilleos C., Hezka J., Lazarou Y., Othonos K.,
RA Demetriades I., Kostrikis L.G.;
RT "Molecular Characterization of HIV Type 1 Strains from Newly Diagnosed
RT Patients in Cyprus (2007-2009) Recovers Multiple Clades Including Unique
RT Recombinant Strains and Lack of Transmitted Drug Resistance.";
RL AIDS Res. Hum. Retroviruses 27:1183-1199(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; JF683781; AEB52792.1; -; Genomic_DNA.
DR Proteomes; UP000120630; 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 74..143
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 197..387
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 587..710
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 716..757
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 767..917
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 936..983
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 936..983
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 1..35
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AEB52792.1"
SQ SEQUENCE 1001 AA; 113707 MW; 259138234A57FE0A CRC64;
FFREDLAFPQ GKAREFPPAQ TRANSPTRGE LQVWGRDNTE AGADRQRTVS SFDFPQISLW
QRPLVTIKIG GQLKEALLDT GADDTVLEEM TLPGKWKPKM IGGIGGFIKV KQYDQILIEI
CGHKVIGTVL VGPTPVNIIG RNLLTQLGCT LNFPISPIET VPVKLKPGMD GPKVKQWPLT
EEKIKALVEI CTEMEKEGKI SKIGPENPYN TPVFAIKKKD STKWRKLVDF RELNKRTQDF
WEVQLGIPHP SGLKKKKSVT VLDVGDAYFS VPLDKEFRKY TAFTIPSINN ATPGVRYQYN
VLPQGWKGSP AIFQSSMTKI LEPFRRQNPD IVIYQYMDDL YVGSDLEIGQ HRTKIEELRL
HLLKWGFTTP DKKHQKEPPF LWMGYELHPD KWTVQPIELP EKDSWTVNDI QKLVGKLNWA
SQIYPGIKVK QLCKLLRGAK ALTEVISLTK EAELELAENR EIIKEPVHGV YYDPSKDLIA
EIQKQEQGQW TYQIYQEPFK NLKTGKYARM RGAHTNDIKQ LTEAVQKIST EGIVIWGKIP
KFKLPIQKET WEAWWTEYWQ ATWIPEWEFV NTPPLVKLWY QLEKEPIVGA ETFYVDGAAN
RETKLGKAGY VTNRGRQRVV SLTDTTNQKT ELQAIYLALQ DSGLEVNIVT DSQYALGIIQ
AQPDKSESEL VSQIIEQLIK KEKVYLTWVP AHKGIGGNEQ VDKLVSTGIR KVLFLDGIDK
AQEEHEKYHN NWRAMASDFN LPPVVAKEIV ASCDKCQLKG EAMHGQVDCS PGIWQLDCTH
VEGKVILVAV HVASGYIEAE VIPAETGQET AYFLLKLAGR WPVKTVHTDN GSNFTSNVVK
AACWWAGIKQ EFGIPYNPQS QGVVESMNKE LKKIIEQVRD QAEHLKTAVQ MAVFIHNFKR
KGGIGGYSAG ERIVDIIATD IQIRELQKQI TKIQNFRVYY RDSRDPLWKG PAKLLWKGEG
AVVIQDNSEI KVVPRRKAKI IRDYGKQMAG DDCVASRQDE D
//
