POL_SFV3L
ID POL_SFV3L Reviewed; 1143 AA.
AC P27401;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2006, sequence version 2.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Pro-Pol polyprotein;
DE AltName: Full=Pr125Pol;
DE Contains:
DE RecName: Full=Protease/Reverse transcriptase/ribonuclease H;
DE EC=2.7.7.49;
DE EC=2.7.7.7;
DE EC=3.1.26.4;
DE EC=3.4.23.-;
DE AltName: Full=p87Pro-RT-RNaseH;
DE Contains:
DE RecName: Full=Protease/Reverse transcriptase;
DE EC=2.7.7.49;
DE EC=2.7.7.7;
DE EC=3.4.23.-;
DE AltName: Full=p65Pro-RT;
DE Contains:
DE RecName: Full=Ribonuclease H;
DE Short=RNase H;
DE EC=3.1.26.4;
DE Contains:
DE RecName: Full=Integrase;
DE Short=IN;
DE EC=2.7.7.- {ECO:0000250|UniProtKB:Q87040};
DE EC=3.1.-.- {ECO:0000250|UniProtKB:Q87040};
DE AltName: Full=p42In;
GN Name=pol;
OS Simian foamy virus type 3 (strain LK3) (SFVagm) (SFV-3).
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Spumaretrovirinae; Spumavirus.
OX NCBI_TaxID=11644;
OH NCBI_TaxID=9534; Chlorocebus aethiops (Green monkey) (Cercopithecus aethiops).
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1310187; DOI=10.1016/0042-6822(92)90026-l;
RA Renne R., Friedl E., Schweizer M., Fleps U., Turek R., Neumann-Haefelin D.;
RT "Genomic organization and expression of simian foamy virus type 3 (SFV-
RT 3).";
RL Virology 186:597-608(1992).
RN [2]
RP REVIEW.
RX PubMed=12908768; DOI=10.1007/978-3-642-55701-9_3;
RA Fluegel R.M., Pfrepper K.-I.;
RT "Proteolytic processing of foamy virus Gag and Pol proteins.";
RL Curr. Top. Microbiol. Immunol. 277:63-88(2003).
RN [3]
RP REVIEW.
RX PubMed=15358259; DOI=10.1016/j.mib.2004.06.009;
RA Delelis O., Lehmann-Che J., Saib A.;
RT "Foamy viruses-a world apart.";
RL Curr. Opin. Microbiol. 7:400-406(2004).
CC -!- FUNCTION: The aspartyl protease activity mediates proteolytic cleavages
CC of Gag and Pol polyproteins. The reverse transcriptase (RT) activity
CC converts the viral RNA genome into dsDNA in the cytoplasm, shortly
CC after virus entry into the cell (early reverse transcription) or after
CC proviral DNA transcription (late reverse transcription). RT consists of
CC a DNA polymerase activity that can copy either DNA or RNA templates,
CC and a ribonuclease H (RNase H) activity that cleaves the RNA strand of
CC RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic
CC mode. Conversion of viral genomic RNA into dsDNA requires many steps. A
CC tRNA-Lys1,2 binds to the primer-binding site (PBS) situated at the 5'-
CC end of the viral RNA. RT uses the 3' end of the tRNA primer to perform
CC a short round of RNA-dependent minus-strand DNA synthesis. The reading
CC proceeds through the U5 region and ends after the repeated (R) region
CC which is present at both ends of viral RNA. The portion of the RNA-DNA
CC heteroduplex is digested by the RNase H, resulting in a ssDNA product
CC attached to the tRNA primer. This ssDNA/tRNA hybridizes with the
CC identical R region situated at the 3' end of viral RNA. This template
CC exchange, known as minus-strand DNA strong stop transfer, can be either
CC intra- or intermolecular. RT uses the 3' end of this newly synthesized
CC short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of
CC the whole template. RNase H digests the RNA template except for a
CC polypurine tract (PPT) situated at the 5'-end and near the center of
CC the genome. It is not clear if both polymerase and RNase H activities
CC are simultaneous. RNase H probably can proceed both in a polymerase-
CC dependent (RNA cut into small fragments by the same RT performing DNA
CC synthesis) and a polymerase-independent mode (cleavage of remaining RNA
CC fragments by free RTs). Secondly, RT performs DNA-directed plus-strand
CC DNA synthesis using the PPT that has not been removed by RNase H as
CC primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5'
CC ssDNA PBS regions hybridize to form a circular dsDNA intermediate.
CC Strand displacement synthesis by RT to the PBS and PPT ends produces a
CC blunt ended, linear dsDNA copy of the viral genome that includes long
CC terminal repeats (LTRs) at both ends (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Integrase catalyzes viral DNA integration into the host
CC chromosome, by performing a series of DNA cutting and joining
CC reactions. This enzyme activity takes place after virion entry into a
CC cell and reverse transcription of the RNA genome in dsDNA. The first
CC step in the integration process is 3' processing. This step requires a
CC complex comprising at least the viral genome, matrix protein, and
CC integrase. This complex is called the pre-integration complex (PIC).
CC The integrase protein removes 2 nucleotides from the 3' end of the
CC viral DNA right (U5) end, leaving the left (U3) intact. In the second
CC step, the PIC enters cell nucleus. This process is mediated through the
CC integrase and allows the virus to infect both dividing (nuclear
CC membrane disassembled) and G1/S-arrested cells (active translocation),
CC but with no viral gene expression in the latter. In the third step,
CC termed strand transfer, the integrase protein joins the previously
CC processed 3' ends to the 5' ends of strands of target cellular DNA at
CC the site of integration. It is however not clear how integration then
CC proceeds to resolve the asymmetrical cleavage of viral DNA (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00408};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.49; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00405};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium ions for reverse transcriptase polymerase
CC activity. {ECO:0000250};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium ions for ribonuclease H (RNase H) activity.
CC Substrate-binding is a precondition for magnesium binding.
CC {ECO:0000250};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Magnesium ions are required for integrase activity. Binds at least
CC 1, maybe 2 magnesium ions. {ECO:0000250};
CC -!- SUBUNIT: The protease is a homodimer, whose active site consists of two
CC apposed aspartic acid residues. {ECO:0000255|PROSITE-ProRule:PRU00863}.
CC -!- SUBCELLULAR LOCATION: [Integrase]: Virion {ECO:0000305}. Host nucleus
CC {ECO:0000250}. Host cytoplasm {ECO:0000305}. Note=Nuclear at initial
CC phase, cytoplasmic at assembly. {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Protease/Reverse transcriptase/ribonuclease H]:
CC Host nucleus {ECO:0000250}. Host cytoplasm {ECO:0000305}. Note=Nuclear
CC at initial phase, cytoplasmic at assembly. {ECO:0000305}.
CC -!- DOMAIN: The reverse transcriptase/ribonuclease H (RT) is structured in
CC five subdomains: finger, palm, thumb, connection and RNase H. Within
CC the palm subdomain, the 'primer grip' region is thought to be involved
CC in the positioning of the primer terminus for accommodating the
CC incoming nucleotide. The RNase H domain stabilizes the association of
CC RT with primer-template (By similarity). {ECO:0000250}.
CC -!- DOMAIN: Integrase core domain contains the D-x(n)-D-x(35)-E motif,
CC named for the phylogenetically conserved glutamic acid and aspartic
CC acid residues and the invariant 35 amino acid spacing between the
CC second and third acidic residues. Each acidic residue of the D,D(35)E
CC motif is independently essential for the 3'-processing and strand
CC transfer activities of purified integrase protein (By similarity).
CC {ECO:0000250}.
CC -!- PTM: Specific enzymatic cleavages in vivo by viral protease yield
CC mature proteins. The protease is not cleaved off from Pol. Since
CC cleavage efficiency is not optimal for all sites, long and active
CC p65Pro-RT, p87Pro-RT-RNaseH and even some Pr125Pol are detected in
CC infected cells.
CC -!- MISCELLANEOUS: The reverse transcriptase is an error-prone enzyme that
CC lacks a proof-reading function. High mutations rate is a direct
CC consequence of this characteristic. RT also displays frequent template
CC switching leading to high recombination rate. Recombination mostly
CC occurs between homologous regions of the two copackaged RNA genomes. If
CC these two RNA molecules derive from different viral strains, reverse
CC transcription will give rise to highly recombinated proviral DNAs.
CC -!- MISCELLANEOUS: Foamy viruses are distinct from other retroviruses in
CC many respects. Their protease is active as an uncleaved Pro-Pol
CC protein. Mature particles do not include the usual processed retroviral
CC structural protein (MA, CA and NC), but instead contain two large Gag
CC proteins. Their functional nucleic acid appears to be either RNA or
CC dsDNA (up to 20% of extracellular particles), because they probably
CC proceed either to an early (before integration) or late reverse
CC transcription (after assembly). Foamy viruses have the ability to
CC retrotranspose intracellularly with high efficiency. They bud
CC predominantly into the endoplasmic reticulum (ER) and occasionally at
CC the plasma membrane. Budding requires the presence of Env proteins.
CC Most viral particles probably remain within the infected cell.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA47796.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; M74895; AAA47796.1; ALT_INIT; Genomic_DNA.
DR RefSeq; YP_001956722.2; NC_010820.1.
DR SMR; P27401; -.
DR MEROPS; A09.001; -.
DR GeneID; 6386654; -.
DR KEGG; vg:6386654; -.
DR Proteomes; UP000007217; Genome.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
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 GO; GO:0075732; P:viral penetration into host nucleus; IEA:UniProtKB-KW.
DR Gene3D; 2.40.70.10; -; 1.
DR Gene3D; 3.30.420.10; -; 2.
DR Gene3D; 3.30.70.270; -; 2.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR041588; Integrase_H2C2.
DR InterPro; IPR021109; Peptidase_aspartic_dom_sf.
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; IPR040903; SH3_11.
DR InterPro; IPR001641; Spumavirus_A9.
DR Pfam; PF17921; Integrase_H2C2; 1.
DR Pfam; PF00075; RNase_H; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF00078; RVT_1; 1.
DR Pfam; PF18103; SH3_11; 1.
DR Pfam; PF03539; Spuma_A9PTase; 1.
DR PRINTS; PR00920; SPUMVIRPTASE.
DR SUPFAM; SSF53098; SSF53098; 2.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS51531; FV_PR; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
DR PROSITE; PS50879; RNASE_H_1; 1.
DR PROSITE; PS50878; RT_POL; 1.
PE 3: Inferred from homology;
KW Aspartyl protease; DNA integration; DNA recombination;
KW DNA-directed DNA polymerase; Endonuclease; Host cytoplasm; Host nucleus;
KW Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotidyltransferase; Protease; Reference proteome; RNA-binding;
KW RNA-directed DNA polymerase; Transferase; Viral genome integration;
KW Viral penetration into host nucleus; Virion; Virus entry into host cell.
FT CHAIN 1..1143
FT /note="Pro-Pol polyprotein"
FT /id="PRO_0000125485"
FT CHAIN 1..751
FT /note="Protease/Reverse transcriptase/ribonuclease H"
FT /evidence="ECO:0000250"
FT /id="PRO_0000245451"
FT CHAIN 1..596
FT /note="Protease/Reverse transcriptase"
FT /evidence="ECO:0000250"
FT /id="PRO_0000245452"
FT CHAIN 597..751
FT /note="Ribonuclease H"
FT /evidence="ECO:0000250"
FT /id="PRO_0000245453"
FT CHAIN 752..1143
FT /note="Integrase"
FT /evidence="ECO:0000250"
FT /id="PRO_0000245454"
FT DOMAIN 1..143
FT /note="Peptidase A9"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00863"
FT DOMAIN 186..363
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT DOMAIN 590..748
FT /note="RNase H type-1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT DOMAIN 864..1023
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT ACT_SITE 24
FT /note="For protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00863"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 314
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 315
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 599
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000250"
FT BINDING 646
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000250"
FT BINDING 669
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000250"
FT BINDING 740
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000250"
FT BINDING 873
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000250"
FT BINDING 935
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000250"
FT SITE 596..597
FT /note="Cleavage; by viral protease; partial"
FT /evidence="ECO:0000250"
FT SITE 751..752
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1143 AA; 129615 MW; 5E5350D0790CF2F3 CRC64;
MDPLQLLQPL EAEIKGTKLK AHWDSGATIT CVPQAFLEEE VPIKNIWIKT IHGEKEQPVY
YLTFKIQGRK VEAEVISSPY DYILVSPSDI PWLMKKPLQL TTLVPLQEYE ERLLKQTMLT
GSYKEKLQSL FLKYDALWQH WENQVGHRRI KPHHIATGTV NPRPQKQYPI NPKAKASIQT
VINDLLKQGV LIQQNSIMNT PVYPVPKPDG KWRMVLDYRE VNKTIPLIAA QNQHSAGILS
SIFRGKYKTT LDLSNGFWAH SITPESYWLT AFTWLGQQYC WTRLPQGFLN SPALFTADVV
DLLKEVPNVQ VYVDDIYISH DDPREHLEQL EKVFSLLLNA GYVVSLKKSE IAQHEVEFLG
FNITKEGRGL TETFKQKLLN ITPPRDLKQL QSILGLLNFA RNFIPNFSEL VKPLYNIIAT
ANGKYITWTT DNSQQLQNII SMLNSAENLE ERNPEVRLIM KVNTSPSAGY IRFYNEFAKR
PIMYLNYVYT KAEVKFTNTE KLLTTIHKGL IKALDLGMGQ EILVYSPIVS MTKIQKTPLP
ERKALPIRWI TWMSYLEDPR IQFHYDKTLP ELQQVPTVTD DIIAKIKHPS EFSMVFYTDG
SAIKHPNVNK SHNAGMGIAQ VQFKPEFTVI NTWSIPLGDH TAQLAEVAAV EFACKKALKI
DGPVLIVTDS FYVAESVNKE LPYWQSNGFF NNKKKPLKHV SKWKSIADCI QLKPDIIIIH
EKGHQPTAST FHTEGNNLAD KLATQGSYVV NINTTPSLDA ELDQLLQGQY PKGFPKHYQY
QLENGQVMVT RPNGKRIIPP KSDRPQIILQ AHNIAHTGRD STFLKVSSKY WWPNLRKDVV
KVIRQCKQCL VTNAATLAAP PILRPERPVK PFDKFFIDYI GPLPPSNGYL HVLVVVDSMT
GFVWLYPTKA PSTSATVKAL NMLTSIAVPK VIHSDQGAAF TSATFADWAK NKGIQLEFST
PYHPQSSGKV ERKNSDIKRL LTKLLVGRPA KWYDLLPVVQ LALNNSYSPS SKYTPHQLLF
GIDSNTPFAN SDTLDLSREE ELSLLQEIRS SLYLPSTPPA SIRAWSPSVG QLVQERVARP
ASLRPRWHKP TPVLEVINPR AVVILDHLGN RRTVSVDNLK LTAYQKDGTP NESAAVVAME
KDE
