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Pro-Pol polyprotein (Pr125Pol) [Cleaved into: Protease/Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (EC 3.4.23.-) (p87Pro-RT-RNaseH); Protease/Reverse transcriptase (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.4.23.-) (p65Pro-RT); Ribonuclease H (RNase H) (EC 3.1.26.4); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-) (p42In)]

 POL_SFV3L               Reviewed;        1143 AA.
P27401;
01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
11-JUL-2006, sequence version 2.
20-JUN-2018, entry version 129.
RecName: Full=Pro-Pol polyprotein;
AltName: Full=Pr125Pol;
Contains:
RecName: Full=Protease/Reverse transcriptase/ribonuclease H;
EC=2.7.7.49;
EC=2.7.7.7;
EC=3.1.26.4;
EC=3.4.23.-;
AltName: Full=p87Pro-RT-RNaseH;
Contains:
RecName: Full=Protease/Reverse transcriptase;
EC=2.7.7.49;
EC=2.7.7.7;
EC=3.4.23.-;
AltName: Full=p65Pro-RT;
Contains:
RecName: Full=Ribonuclease H;
Short=RNase H;
EC=3.1.26.4;
Contains:
RecName: Full=Integrase;
Short=IN;
EC=2.7.7.- {ECO:0000250|UniProtKB:Q87040};
EC=3.1.-.- {ECO:0000250|UniProtKB:Q87040};
AltName: Full=p42In;
Name=pol;
Simian foamy virus type 3 (strain LK3) (SFVagm) (SFV-3).
Viruses; Ortervirales; Retroviridae; Spumaretrovirinae; Spumavirus.
NCBI_TaxID=11644;
NCBI_TaxID=9534; Chlorocebus aethiops (Green monkey) (Cercopithecus aethiops).
NCBI_TaxID=9606; Homo sapiens (Human).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=1310187; DOI=10.1016/0042-6822(92)90026-L;
Renne R., Friedl E., Schweizer M., Fleps U., Turek R.,
Neumann-Haefelin D.;
"Genomic organization and expression of simian foamy virus type 3
(SFV-3).";
Virology 186:597-608(1992).
[2]
REVIEW.
PubMed=12908768;
Fluegel R.M., Pfrepper K.-I.;
"Proteolytic processing of foamy virus Gag and Pol proteins.";
Curr. Top. Microbiol. Immunol. 277:63-88(2003).
[3]
REVIEW.
PubMed=15358259; DOI=10.1016/j.mib.2004.06.009;
Delelis O., Lehmann-Che J., Saib A.;
"Foamy viruses-a world apart.";
Curr. Opin. Microbiol. 7:400-406(2004).
-!- FUNCTION: The aspartyl protease activity mediates proteolytic
cleavages of Gag and Pol polyproteins. The reverse transcriptase
(RT) activity converts the viral RNA genome into dsDNA in the
cytoplasm, shortly after virus entry into the cell (early reverse
transcription) or after proviral DNA transcription (late reverse
transcription). RT consists of a DNA polymerase activity that can
copy either DNA or RNA templates, and a ribonuclease H (RNase H)
activity that cleaves the RNA strand of RNA-DNA heteroduplexes in
a partially processive 3' to 5' endonucleasic mode. Conversion of
viral genomic RNA into dsDNA requires many steps. A tRNA-Lys1,2
binds to the primer-binding site (PBS) situated at the 5'-end of
the viral RNA. RT uses the 3' end of the tRNA primer to perform a
short round of RNA-dependent minus-strand DNA synthesis. The
reading proceeds through the U5 region and ends after the repeated
(R) region which is present at both ends of viral RNA. The portion
of the RNA-DNA heteroduplex is digested by the RNase H, resulting
in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA
hybridizes with the identical R region situated at the 3' end of
viral RNA. This template exchange, known as minus-strand DNA
strong stop transfer, can be either intra- or intermolecular. RT
uses the 3' end of this newly synthesized short ssDNA to perform
the RNA-dependent minus-strand DNA synthesis of the whole
template. RNase H digests the RNA template except for a polypurine
tract (PPT) situated at the 5'-end and near the center of the
genome. It is not clear if both polymerase and RNase H activities
are simultaneous. RNase H probably can proceed both in a
polymerase-dependent (RNA cut into small fragments by the same RT
performing DNA synthesis) and a polymerase-independent mode
(cleavage of remaining RNA fragments by free RTs). Secondly, RT
performs DNA-directed plus-strand DNA synthesis using the PPT that
has not been removed by RNase H as primer. PPT and tRNA primers
are then removed by RNase H. The 3' and 5' ssDNA PBS regions
hybridize to form a circular dsDNA intermediate. Strand
displacement synthesis by RT to the PBS and PPT ends produces a
blunt ended, linear dsDNA copy of the viral genome that includes
long terminal repeats (LTRs) at both ends (By similarity).
{ECO:0000250}.
-!- FUNCTION: Integrase catalyzes viral DNA integration into the host
chromosome, by performing a series of DNA cutting and joining
reactions. This enzyme activity takes place after virion entry
into a cell and reverse transcription of the RNA genome in dsDNA.
The first step in the integration process is 3' processing. This
step requires a complex comprising at least the viral genome,
matrix protein, and integrase. This complex is called the pre-
integration complex (PIC). The integrase protein removes 2
nucleotides from the 3' end of the viral DNA right (U5) end,
leaving the left (U3) intact. In the second step, the PIC enters
cell nucleus. This process is mediated through the integrase and
allows the virus to infect both dividing (nuclear membrane
disassembled) and G1/S-arrested cells (active translocation), but
with no viral gene expression in the latter. In the third step,
termed strand transfer, the integrase protein joins the previously
processed 3' ends to the 5' ends of strands of target cellular DNA
at the site of integration. It is however not clear how
integration then proceeds to resolve the asymmetrical cleavage of
viral DNA (By similarity). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester. {ECO:0000255|PROSITE-ProRule:PRU00408}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00405}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 2 magnesium ions for reverse transcriptase polymerase
activity. {ECO:0000250};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 2 magnesium ions for ribonuclease H (RNase H) activity.
Substrate-binding is a precondition for magnesium binding.
{ECO:0000250};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Magnesium ions are required for integrase activity. Binds at
least 1, maybe 2 magnesium ions. {ECO:0000250};
-!- SUBUNIT: The protease is a homodimer, whose active site consists
of two apposed aspartic acid residues. {ECO:0000255|PROSITE-
ProRule:PRU00863}.
-!- SUBCELLULAR LOCATION: Integrase: Virion {ECO:0000305}. Host
nucleus {ECO:0000250}. Host cytoplasm {ECO:0000305}. Note=Nuclear
at initial phase, cytoplasmic at assembly. {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Protease/Reverse transcriptase/ribonuclease
H: Host nucleus {ECO:0000250}. Host cytoplasm {ECO:0000305}.
Note=Nuclear at initial phase, cytoplasmic at assembly.
{ECO:0000305}.
-!- DOMAIN: The reverse transcriptase/ribonuclease H (RT) is
structured in five subdomains: finger, palm, thumb, connection and
RNase H. Within the palm subdomain, the "primer grip" region is
thought to be involved in the positioning of the primer terminus
for accommodating the incoming nucleotide. The RNase H domain
stabilizes the association of RT with primer-template (By
similarity). {ECO:0000250}.
-!- DOMAIN: Integrase core domain contains the D-x(n)-D-x(35)-E motif,
named for the phylogenetically conserved glutamic acid and
aspartic acid residues and the invariant 35 amino acid spacing
between the second and third acidic residues. Each acidic residue
of the D,D(35)E motif is independently essential for the 3'-
processing and strand transfer activities of purified integrase
protein (By similarity). {ECO:0000250}.
-!- PTM: Specific enzymatic cleavages in vivo by viral protease yield
mature proteins. The protease is not cleaved off from Pol. Since
cleavage efficiency is not optimal for all sites, long and active
p65Pro-RT, p87Pro-RT-RNaseH and even some Pr125Pol are detected in
infected cells.
-!- MISCELLANEOUS: The reverse transcriptase is an error-prone enzyme
that lacks a proof-reading function. High mutations rate is a
direct consequence of this characteristic. RT also displays
frequent template switching leading to high recombination rate.
Recombination mostly occurs between homologous regions of the two
copackaged RNA genomes. If these two RNA molecules derive from
different viral strains, reverse transcription will give rise to
highly recombinated proviral DNAs.
-!- MISCELLANEOUS: Foamy viruses are distinct from other retroviruses
in many respects. Their protease is active as an uncleaved Pro-Pol
protein. Mature particles do not include the usual processed
retroviral structural protein (MA, CA and NC), but instead contain
two large Gag proteins. Their functional nucleic acid appears to
be either RNA or dsDNA (up to 20% of extracellular particles),
because they probably proceed either to an early (before
integration) or late reverse transcription (after assembly). Foamy
viruses have the ability to retrotranspose intracellularly with
high efficiency. They bud predominantly into the endoplasmic
reticulum (ER) and occasionally at the plasma membrane. Budding
requires the presence of Env proteins. Most viral particles
probably remain within the infected cell.
-!- SEQUENCE CAUTION:
Sequence=AAA47796.1; Type=Erroneous initiation; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; M74895; AAA47796.1; ALT_INIT; Genomic_DNA.
RefSeq; YP_001956722.2; NC_010820.1.
ProteinModelPortal; P27401; -.
SMR; P27401; -.
MEROPS; A09.001; -.
PRIDE; P27401; -.
GeneID; 6386654; -.
KEGG; vg:6386654; -.
OrthoDB; VOG090000AJ; -.
Proteomes; UP000007217; Genome.
GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
GO; GO:0019012; C:virion; IEA:UniProtKB-SubCell.
GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
GO; GO:0075732; P:viral penetration into host nucleus; IEA:UniProtKB-KW.
Gene3D; 2.40.70.10; -; 1.
Gene3D; 3.30.420.10; -; 2.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR021109; Peptidase_aspartic_dom_sf.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR002156; RNaseH_domain.
InterPro; IPR036397; RNaseH_sf.
InterPro; IPR000477; RT_dom.
InterPro; IPR001641; Spumavirus_A9.
Pfam; PF00075; RNase_H; 1.
Pfam; PF00665; rve; 1.
Pfam; PF00078; RVT_1; 1.
Pfam; PF03539; Spuma_A9PTase; 1.
PRINTS; PR00920; SPUMVIRPTASE.
ProDom; PD013079; Peptidase_A9_cat; 1.
SUPFAM; SSF53098; SSF53098; 2.
PROSITE; PS51531; FV_PR; 1.
PROSITE; PS50994; INTEGRASE; 1.
PROSITE; PS50879; RNASE_H; 1.
PROSITE; PS50878; RT_POL; 1.
3: Inferred from homology;
Aspartyl protease; Complete proteome; DNA integration;
DNA recombination; DNA-directed DNA polymerase; Endonuclease;
Host cytoplasm; Host nucleus; Hydrolase; Magnesium; Metal-binding;
Multifunctional enzyme; Nuclease; Nucleotidyltransferase; Protease;
RNA-binding; RNA-directed DNA polymerase; Transferase;
Viral genome integration; Viral penetration into host nucleus; Virion;
Virus entry into host cell.
CHAIN 1 1143 Pro-Pol polyprotein.
/FTId=PRO_0000125485.
CHAIN 1 751 Protease/Reverse
transcriptase/ribonuclease H.
{ECO:0000250}.
/FTId=PRO_0000245451.
CHAIN 1 596 Protease/Reverse transcriptase.
{ECO:0000250}.
/FTId=PRO_0000245452.
CHAIN 597 751 Ribonuclease H. {ECO:0000250}.
/FTId=PRO_0000245453.
CHAIN 752 1143 Integrase. {ECO:0000250}.
/FTId=PRO_0000245454.
DOMAIN 1 143 Peptidase A9. {ECO:0000255|PROSITE-
ProRule:PRU00863}.
DOMAIN 186 363 Reverse transcriptase.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
DOMAIN 590 748 RNase H. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
DOMAIN 864 1023 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
COMPBIAS 716 719 Poly-Ile.
ACT_SITE 24 24 For protease activity.
{ECO:0000255|PROSITE-ProRule:PRU00863}.
METAL 252 252 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 314 314 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 315 315 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 599 599 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 646 646 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 669 669 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 740 740 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 873 873 Magnesium; catalytic; for integrase
activity. {ECO:0000250}.
METAL 935 935 Magnesium; catalytic; for integrase
activity. {ECO:0000250}.
SITE 596 597 Cleavage; by viral protease; partial.
{ECO:0000250}.
SITE 751 752 Cleavage; by viral protease.
{ECO:0000250}.
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


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