ID Q2NN51_9HIV1 Unreviewed; 1003 AA.
AC Q2NN51;
DT 07-FEB-2006, integrated into UniProtKB/TrEMBL.
DT 07-FEB-2006, sequence version 1.
DT 27-MAR-2024, entry version 115.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AAX32950.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AAX32950.1};
OS Human immunodeficiency virus 1.
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11676 {ECO:0000313|EMBL:AAX32950.1, ECO:0000313|Proteomes:UP000132085};
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1] {ECO:0000313|EMBL:AAX32950.1, ECO:0000313|Proteomes:UP000132085}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=5084-83 {ECO:0000313|EMBL:AAX32950.1};
RA Mikhail M., Wang B., Lemey P., Lal R.B., Yang C., Vandamme A.-M.,
RA Owen S.M., Spira T., Saksena N.K.;
RT "Full length genome analysis of HIV-1 viral evolution, and date of origin
RT in an American cohort.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
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; AY835754; AAX32950.1; -; Genomic_DNA.
DR MEROPS; A02.001; -.
DR Proteomes; UP000132085; 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 76..145
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 199..389
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 589..712
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 718..759
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 769..919
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 938..985
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 938..985
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AAX32950.1"
SQ SEQUENCE 1003 AA; 113751 MW; DDA9F248FA625FAB CRC64;
FFREDLAFLQ GKAREFSSEQ TRANSPTRRK LQVWGRDNNS LSEAGAERQG TVSFNFPQIT
LWQRPLVTIK IGGQLKEALL DTGADDTVLE EMNLPGRWKP KMIGGIGGFI KVRQYDQILI
EICGHKAIGT VLVGPTPVNI IGRNLLTQIG CTLNFPISPI ETVPVKLKPG MDGPKVKQWP
LTEEKIKALV EICTEMEQEG KISRIGPENP YNTPVFAIKK KDSTKWRKLV DFRELNKRTQ
DFWEVQLGIP HPAGLKKKKS VTVLDVGDAY FSVPLDKDFR KYTAFTIPSI NNETPGIRYQ
YNVLPQGWKG SPAIFQSSMT KILEPFRKQN PDVVIYQYMD DLYVGSDLEI GRHGTKIEEL
RQHLLRWGFT TPDKKHQKEP PFLWMGYELH PDKWTVQPIV LPEKDSWTVN DIQKLVGKLN
WASQIYAGIK VRQLCKLLRG TKALTEVIPL TKEAELELAE NREILKEPVH GVYYDPSKDL
IVEIQKQGQG QWTYQIYQEP FKNLKTGKYA RMRGAHTNDV KQLTEAVQKI TTESIVIWGK
TPKFRLPIQK ETWEAWWTEY WQATWIPEWE FVNTPPLVKL WYQLEKEPIV GAETFYVDGA
ANRETKLGKA GYVTDRGRQK VVPLTDTTNQ KTELQAIHLA LQDSGLEVNI VTDSQYALGI
IQAQPDKSES ELVSQIIEQL IKKEKVYLAW VPAHKGIGGN EQVDKLVSAG IRKVLFLDGI
DKAQDEHERY HSNWRAMASD FNLPPVVAKE IVASCDKCQL KGEAMHGQVD CSPGIWQLDC
THLEGKVILV AVHVASGYIE AEVIPAETGQ ETAYFLLKLA GRWPVKTIHT DNGGNFISTA
VKAACWWAGI KQEFGIPYNP QSQGVVESIN KELKKIIGQV RDQAEHLKTA VQMAVFIHNF
KRKGGIGGYS AGERIIDIIA TDIQTKELQK QITKIQNFRV YYRDSRDPLW KGPAKLLWKG
EGAVVIQDNS DIKVVPRRKA KIIRDYGKQM AGDDCVASTR DED
//
