ID Q5QGH9_SIV Unreviewed; 1060 AA.
AC Q5QGH9;
DT 04-JAN-2005, integrated into UniProtKB/TrEMBL.
DT 04-JAN-2005, sequence version 1.
DT 27-MAR-2024, entry version 143.
DE SubName: Full=Pol protein {ECO:0000313|EMBL:AAV65312.1};
DE Flags: Fragment;
GN Name=pol {ECO:0000313|EMBL:AAV65312.1};
OS Simian immunodeficiency virus (SIV).
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX NCBI_TaxID=11723 {ECO:0000313|EMBL:AAV65312.1};
OH NCBI_TaxID=9527; Cercopithecidae (Old World monkeys).
OH NCBI_TaxID=9598; Pan troglodytes (Chimpanzee).
RN [1] {ECO:0007829|PDB:2SAM}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 117-208.
RX PubMed=8241141; DOI=10.1021/bi00097a030;
RA Rose R.B., Rose J.R., Salto R., Craik C.S., Stroud R.M.;
RT "Structure of the protease from simian immunodeficiency virus: complex with
RT an irreversible nonpeptide inhibitor.";
RL Biochemistry 32:12498-12507(1993).
RN [2] {ECO:0000313|EMBL:AAV65312.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=SIVmac239 {ECO:0000313|EMBL:AAV65312.1};
RX PubMed=15564508; DOI=10.1128/JVI.78.24.14012-14022.2004;
RA O'Connor D.H., McDermott A.B., Krebs K.C., Dodds E.J., Miller J.E.,
RA Gonzalez E.J., Jacoby T.J., Yant L., Piontkivska H., Pantophlet R.,
RA Burton D.R., Rehrauer W.M., Wilson N., Hughes A.L., Watkins D.I.;
RT "A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency
RT virus sequence variation.";
RL J. Virol. 78:14012-14022(2004).
RN [3] {ECO:0007829|PDB:3RWE, ECO:0007829|PDB:3RWH}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 435-443.
RX PubMed=22084443; DOI=10.4049/jimmunol.1101726;
RA Wu Y., Gao F., Liu J., Qi J., Gostick E., Price D.A., Gao G.F.;
RT "Structural basis of diverse peptide accommodation by the rhesus macaque
RT MHC class I molecule Mamu-B*17: insights into immune protection from simian
RT immunodeficiency virus.";
RL J. Immunol. 187:6382-6392(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; AY588945; AAV65312.1; -; Genomic_RNA.
DR PDB; 2SAM; X-ray; 2.40 A; A=110-208.
DR PDB; 3RWE; X-ray; 2.40 A; C=435-443.
DR PDB; 3RWH; X-ray; 2.60 A; C/F=372-379.
DR PDBsum; 2SAM; -.
DR PDBsum; 3RWE; -.
DR PDBsum; 3RWH; -.
DR SMR; Q5QGH9; -.
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 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 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:2SAM, ECO:0007829|PDB:3RWE};
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 129..198
FT /note="Peptidase A2"
FT /evidence="ECO:0000259|PROSITE:PS50175"
FT DOMAIN 252..442
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 641..764
FT /note="RNase H type-1"
FT /evidence="ECO:0000259|PROSITE:PS50879"
FT DOMAIN 770..811
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS50876"
FT DOMAIN 820..971
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT DOMAIN 990..1037
FT /note="Integrase-type"
FT /evidence="ECO:0000259|PROSITE:PS51027"
FT DNA_BIND 990..1037
FT /note="Integrase-type"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00506"
FT REGION 42..78
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1041..1060
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AAV65312.1"
SQ SEQUENCE 1060 AA; 120129 MW; 85F66FA6162FB98F CRC64;
VLELWERGTL CKAMQSPKKT GMLEMWKNGP CYGQMPRQTG GFFRPWSMGK EAPQFPHGSS
ASGADANCSP RGPSCGSAKE LHAVGQAAER KAERKQREAL QGGDRGFAAP QFSLWRRPVV
TAHIEGQPVE VLLDTGADDS IVTGIELGPH YTPKIVGGIG GFINTKEYKN VEIEVLGKRI
KGTIMTGDTP INIFGRNLLT ALGMSLNFPI AKVEPVKVAL KPGKDGPKLK QWPLSKEKIV
ALREICEKME KDGQLEEAPP TNPYNTPTFA IKKKDKNKWR MLIDFRELNR VTQDFTEVQL
GIPHPAGLAK RKRITVLDIG DAYFSIPLDE EFRQYTAFTL PSVNNAEPGK RYIYKVLPQG
WKGSPAIFQY TMRHVLEPFR KANPDVTLVQ YMDDILIASD RTDLEHDRVV LQXKELLNSI
GFSTPEEKFQ KDPPFQWMGY ELWPTKWKLQ KIELPQRETW TVNDIQKLVG VLNWAAQIYP
GIKTKHLCRL IRGKMTLTEE VQWTEMAEAE YEENKIILSQ EQEGCYYQEG KPLEATVIKS
QDNQWSYKIH QEDKILKVGK FAKIKNTHTN GVRLLAHVIQ KIGKEAIVIW GQVPKFHLPV
EKDVWEQWWT DYWQVTWIPE WDFISTPPLV RLVFNLVKDP IEGEETYYTD GSCNKQSKEG
KAGYITDRGK DKVKVLEQTT NQQAELEAFL MALTDSGPKA NIIVDSQYVM GIITGCPTES
ESRLVNQIIE EMIKKSEIYV AWVPAHKGIG GNQEIDHLVS QGIRQVLFLE KIEPAQEEHD
KYHSNVKELV FKFGLPRIVA RQIVDTCDKC HQKGEAIHGQ ANSDLGTWQM DCTHLEGKII
IVAVHVASGF IEAEVIPQET GRQTALFLLK LAGRWPITHL HTDNGANFAS QEVKMVAWWA
GIEHTFGVPY NPQSQGVVEA MNHHLKNQID RIREQANSVE TIVLMAVHCM NFKRRGGIGD
MTPAERLINM ITTEQEIQFQ QSKNSKFKNF RVYYREGRDQ LWKGPGELLW KGEGAVILKV
GTDIKVVPRR KAKIIKDYGG GKEVDSSSHM EDTGEAREVA
//
