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Gag-Pro-Pol polyprotein [Cleaved into: Matrix protein p15 (MA); Capsid protein p24 (CA); Nucleocapsid protein p12-pro; Protease (EC 3.4.23.-); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]

 POL_BLVAU               Reviewed;        1416 AA.
P25059;
01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
20-DEC-2017, sequence version 2.
05-DEC-2018, entry version 94.
RecName: Full=Gag-Pro-Pol polyprotein;
Contains:
RecName: Full=Matrix protein p15;
Short=MA;
Contains:
RecName: Full=Capsid protein p24;
Short=CA;
Contains:
RecName: Full=Nucleocapsid protein p12-pro;
Contains:
RecName: Full=Protease;
EC=3.4.23.- {ECO:0000255|PROSITE-ProRule:PRU00275};
Contains:
RecName: Full=Reverse transcriptase/ribonuclease H;
Short=RT;
EC=2.7.7.49 {ECO:0000255|PROSITE-ProRule:PRU00405};
EC=2.7.7.7 {ECO:0000255|PROSITE-ProRule:PRU00405};
EC=3.1.26.4 {ECO:0000255|PROSITE-ProRule:PRU00408};
Contains:
RecName: Full=Integrase;
Short=IN;
EC=2.7.7.- {ECO:0000250|UniProtKB:P03363};
EC=3.1.-.- {ECO:0000250|UniProtKB:P03363};
Name=pol;
Bovine leukemia virus (isolate Australian) (BLV).
Viruses; Ortervirales; Retroviridae; Orthoretrovirinae;
Deltaretrovirus.
NCBI_TaxID=11903;
NCBI_TaxID=9913; Bos taurus (Bovine).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=2167927; DOI=10.1099/0022-1317-71-8-1737;
Coulston J., Naif H., Brandon R., Kumar S., Khan S., Daniel R.C.W.,
Lavin M.F.;
"Molecular cloning and sequencing of an Australian isolate of proviral
bovine leukaemia virus DNA: comparison with other isolates.";
J. Gen. Virol. 71:1737-1746(1990).
[2]
RIBOSOMAL FRAMESHIFT.
PubMed=6094258;
Sagata N., Yasunaga T., Ikawa Y.;
"Identification of a potential protease-coding gene in the genomes of
bovine leukemia and human T-cell leukemia viruses.";
FEBS Lett. 178:79-82(1984).
[3]
DOMAIN LATE-BUDDING, AND MUTAGENESIS OF 100-PRO--TYR-103.
PubMed=12134053; DOI=10.1128/JVI.76.16.8485-8493.2002;
Wang H., Norris K.M., Mansky L.M.;
"Analysis of bovine leukemia virus gag membrane targeting and late
domain function.";
J. Virol. 76:8485-8493(2002).
-!- FUNCTION: Gag-Pro-Pol polyprotein: The matrix domain targets Gag,
Gag-Pro and Gag-Pro-Pol polyproteins to the plasma membrane via a
multipartite membrane binding signal, that includes its
myristoylated N-terminus. {ECO:0000250|UniProtKB:P03345}.
-!- FUNCTION: Matrix protein p15: Matrix protein.
{ECO:0000250|UniProtKB:P03345}.
-!- FUNCTION: Capsid protein p24: Forms the spherical core of the
virus that encapsulates the genomic RNA-nucleocapsid complex.
{ECO:0000250|UniProtKB:P03362}.
-!- FUNCTION: Nucleocapsid protein p12-pro: Binds strongly to viral
nucleic acids and promote their aggregation. Also destabilizes the
nucleic acids duplexes via highly structured zinc-binding motifs.
{ECO:0000250|UniProtKB:P03345}.
-!- FUNCTION: Protease: The aspartyl protease mediates proteolytic
cleavages of Gag and Gag-Pol polyproteins during or shortly after
the release of the virion from the plasma membrane. Cleavages take
place as an ordered, step-wise cascade to yield mature proteins.
This process is called maturation. Displays maximal activity
during the budding process just prior to particle release from the
cell. {ECO:0000255|PROSITE-ProRule:PRU00275}.
-!- FUNCTION: Reverse transcriptase/ribonuclease H: RT is a
multifunctional enzyme that converts the viral RNA genome into
dsDNA in the cytoplasm, shortly after virus entry into the cell.
This enzyme displays 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-Pro 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 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.
{ECO:0000250}.
-!- FUNCTION: Integrase: Catalyzes viral DNA integration into the host
chromosome, by performing a series of DNA cutting and joining
reactions. {ECO:0000250|UniProtKB:P03362}.
-!- CATALYTIC ACTIVITY:
Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.;
EC=3.1.26.4; Evidence={ECO:0000255|PROSITE-ProRule:PRU00408};
-!- CATALYTIC ACTIVITY:
Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-
COMP:11130, Rhea:RHEA-COMP:11131, ChEBI:CHEBI:33019,
ChEBI:CHEBI:61560, ChEBI:CHEBI:83828; EC=2.7.7.49;
Evidence={ECO:0000255|PROSITE-ProRule:PRU00405};
-!- CATALYTIC ACTIVITY:
Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-
COMP:11130, Rhea:RHEA-COMP:11131, ChEBI:CHEBI:33019,
ChEBI:CHEBI:61560, ChEBI:CHEBI:83828; EC=2.7.7.7;
Evidence={ECO:0000255|PROSITE-ProRule:PRU00405};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|PROSITE-ProRule:PRU00405};
Note=The RT polymerase active site binds 2 magnesium ions.
{ECO:0000255|PROSITE-ProRule:PRU00405};
-!- SUBUNIT: Gag-Pro-Pol polyprotein: Homodimer; the homodimers are
part of the immature particles. Gag-Pro-Pol polyprotein: Interacts
with human TSG101 and NEDD4; these interactions are essential for
budding and release of viral particles. Matrix protein p15:
Homodimer; further assembles as homohexamers.
{ECO:0000250|UniProtKB:P03345}.
-!- SUBCELLULAR LOCATION: Matrix protein p15: Virion
{ECO:0000250|UniProtKB:P03345}.
-!- SUBCELLULAR LOCATION: Capsid protein p24: Virion
{ECO:0000250|UniProtKB:P03345}.
-!- SUBCELLULAR LOCATION: Nucleocapsid protein p12-pro: Virion
{ECO:0000250|UniProtKB:P03345}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=3;
Name=Gag-Pro-Pol polyprotein;
IsoId=P25059-1; Sequence=Displayed;
Note=Produced by -1 ribosomal frameshiftings between gag-pro and
pro-pol. {ECO:0000269|PubMed:6094258};
Name=Gag polyprotein;
IsoId=P25058-1; Sequence=External;
Note=Produced by conventional translation.
{ECO:0000269|PubMed:6094258};
Name=Gag-Pro polyprotein;
IsoId=P0DOI1-1; Sequence=External;
Note=Produced by -1 ribosomal frameshifting between gag-pro.
{ECO:0000269|PubMed:6094258};
-!- DOMAIN: Gag-Pro-Pol polyprotein: Late-budding domains (L domains)
are short sequence motifs essential for viral particle release.
They can occur individually or in close proximity within
structural proteins. They interacts with sorting cellular proteins
of the multivesicular body (MVB) pathway. Most of these proteins
are class E vacuolar protein sorting factors belonging to ESCRT-I,
ESCRT-II or ESCRT-III complexes. Matrix protein p15 contains one L
domain: a PPXY motif which binds to the WW domains of the
ubiquitin ligase NEDD4. {ECO:0000269|PubMed:12134053}.
-!- PTM: Matrix protein p15: Phosphorylation of the matrix protein p15
by MAPK1 seems to play a role in budding.
{ECO:0000250|UniProtKB:P03345}.
-!- PTM: Gag-Pro-Pol polyprotein: Myristoylated. Myristoylation of the
matrix (MA) domain mediates the transport and binding of Gag
polyproteins to the host plasma membrane and is required for the
assembly of viral particles. {ECO:0000250|UniProtKB:P03345}.
-!- PTM: Gag-Pro-Pol polyprotein: Specific enzymatic cleavages by the
viral protease yield mature proteins. The polyprotein is cleaved
during and after budding, this process is termed maturation. The
protease is autoproteolytically processed at its N- and C-termini.
{ECO:0000250|UniProtKB:P03362}.
-!- MISCELLANEOUS: Reverse transcriptase/ribonuclease H: 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 swiching
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. {ECO:0000255|PROSITE-ProRule:PRU00405}.
-!- SIMILARITY: Belongs to the retroviral Pol polyprotein family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAA00544.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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EMBL; D00647; BAA00544.1; ALT_SEQ; Genomic_DNA.
PIR; JQ0555; GNLJGA.
ProteinModelPortal; P25059; -.
GO; GO:0019013; C:viral nucleocapsid; IEA:UniProtKB-KW.
GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-EC.
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:0039660; F:structural constituent of virion; IEA:UniProtKB-KW.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
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:0039702; P:viral budding via host ESCRT complex; 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.
Gene3D; 1.10.1200.30; -; 1.
Gene3D; 1.10.185.10; -; 1.
Gene3D; 1.10.375.10; -; 1.
Gene3D; 2.40.70.10; -; 1.
Gene3D; 3.30.420.10; -; 2.
InterPro; IPR003139; D_retro_matrix.
InterPro; IPR036989; D_retro_matrix_sf.
InterPro; IPR000721; Gag_p24.
InterPro; IPR001037; Integrase_C_retrovir.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR001995; Peptidase_A2_cat.
InterPro; IPR021109; Peptidase_aspartic_dom_sf.
InterPro; IPR018061; Retropepsins.
InterPro; IPR008916; Retrov_capsid_C.
InterPro; IPR008919; Retrov_capsid_N.
InterPro; IPR010999; Retrovr_matrix.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR002156; RNaseH_domain.
InterPro; IPR036397; RNaseH_sf.
InterPro; IPR000477; RT_dom.
InterPro; IPR001878; Znf_CCHC.
InterPro; IPR036875; Znf_CCHC_sf.
Pfam; PF02228; Gag_p19; 1.
Pfam; PF00607; Gag_p24; 1.
Pfam; PF00552; IN_DBD_C; 1.
Pfam; PF00665; rve; 1.
Pfam; PF00077; RVP; 1.
Pfam; PF00078; RVT_1; 1.
Pfam; PF00098; zf-CCHC; 1.
SMART; SM00343; ZnF_C2HC; 2.
SUPFAM; SSF47836; SSF47836; 1.
SUPFAM; SSF47943; SSF47943; 1.
SUPFAM; SSF50630; SSF50630; 1.
SUPFAM; SSF53098; SSF53098; 1.
SUPFAM; SSF57756; SSF57756; 1.
PROSITE; PS50175; ASP_PROT_RETROV; 1.
PROSITE; PS00141; ASP_PROTEASE; 1.
PROSITE; PS50994; INTEGRASE; 1.
PROSITE; PS51027; INTEGRASE_DBD; 1.
PROSITE; PS50879; RNASE_H; 1.
PROSITE; PS50878; RT_POL; 1.
PROSITE; PS50158; ZF_CCHC; 1.
1: Evidence at protein level;
Aspartyl protease; Capsid protein; DNA integration; DNA recombination;
DNA-binding; Endonuclease; Host-virus interaction; Hydrolase;
Lipoprotein; Metal-binding; Multifunctional enzyme; Myristate;
Nuclease; Nucleotidyltransferase; Phosphoprotein; Protease; Repeat;
Ribosomal frameshifting; RNA-directed DNA polymerase; Transferase;
Viral budding; Viral budding via the host ESCRT complexes;
Viral genome integration; Viral matrix protein; Viral nucleoprotein;
Viral release from host cell; Virion; Virus entry into host cell;
Zinc; Zinc-finger.
INIT_MET 1 1 Removed; by host. {ECO:0000255}.
CHAIN 2 1416 Gag-Pro-Pol polyprotein.
/FTId=PRO_0000125481.
CHAIN 2 109 Matrix protein p15.
/FTId=PRO_0000442552.
CHAIN 110 323 Capsid protein p24.
/FTId=PRO_0000442553.
CHAIN 324 419 Nucleocapsid protein p12-pro.
/FTId=PRO_0000442554.
CHAIN 420 545 Protease.
/FTId=PRO_0000442555.
CHAIN 546 1120 Reverse transcriptase/ribonuclease H.
/FTId=PRO_0000442556.
CHAIN 1121 1416 Integrase.
/FTId=PRO_0000442557.
DOMAIN 447 525 Peptidase A2. {ECO:0000255|PROSITE-
ProRule:PRU00275}.
DOMAIN 586 776 Reverse transcriptase.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
DOMAIN 996 1126 RNase H. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
DOMAIN 1179 1343 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
ZN_FING 345 362 CCHC-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 370 387 CCHC-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
DNA_BIND 1352 1400 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00506}.
MOTIF 100 103 PPXY motif.
{ECO:0000269|PubMed:12134053}.
COMPBIAS 560 563 Poly-Pro. {ECO:0000255}.
COMPBIAS 910 914 Poly-Leu. {ECO:0000255}.
ACT_SITE 452 452 Protease; shared with dimeric partner.
{ECO:0000255|PROSITE-ProRule:PRU00275}.
METAL 652 652 Magnesium; catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
METAL 727 727 Magnesium; catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
METAL 728 728 Magnesium; catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
METAL 1005 1005 Magnesium. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1036 1036 Magnesium. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1057 1057 Magnesium. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1118 1118 Magnesium. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1190 1190 Magnesium; catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1247 1247 Magnesium; catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
SITE 109 110 Cleavage; by viral protease.
{ECO:0000250|UniProtKB:P03345}.
SITE 323 324 Cleavage; by viral protease.
{ECO:0000250|UniProtKB:P03345}.
SITE 419 420 Cleavage; by viral protease.
{ECO:0000250|UniProtKB:P03345}.
SITE 544 545 Cleavage; by viral protease.
{ECO:0000250|UniProtKB:P03345}.
SITE 1120 1121 Cleavage; by viral protease.
{ECO:0000250|UniProtKB:P03345}.
LIPID 2 2 N-myristoyl glycine; by host.
{ECO:0000255}.
MUTAGEN 100 103 PPPY->AAAA: Greatly reduced release of
new viral particles.
{ECO:0000269|PubMed:12134053}.
SEQUENCE 1416 AA; 156937 MW; 43542CE5D408581A CRC64;
MGNSPSYNPP AGISPSDWLN LLQSAQRLNP RPSPSDFTDL KNYIHWFHKT QKKPWTFTSG
GPASCPPGKF GRVPLVLATL NEVLSNDEGA PGASAPEEQP PPYDPPAVLP IISEGNRNRH
RAWALRELQD IKKEIENKAP GSQVWIQTLR LAILQADPTP ADLEQLCQYI ASPVDQTAHM
TSLTAAIAAE AANTLQGFNP QNGTLTQQSA QPNAGDLRSQ YQNLWLQAWK NLPTRPSVQP
WSTIVQGPAE SYVEFVNRLQ ISLADNLPDG VPKEPIIDSL SYANANKECQ QILQGRGLVA
APVGQKLQAC AHWAPKTKQP AILVHTPGPK MPGPRQPAPK RPPPGPCYRC LKEGHWARDC
PTKTTGPPPG PCPICKDPSH WKRDCPTLKS KKLIEGGPSA PQIITPITDS LSEAELECLL
SIPLARSRPS VAVYLSGPWL QPSQNQALML VDTGAENTVL PQNWLVRDYP RTPAAVLGAG
GISRNRYNWL QGPLTLALKP EGPFITIPKI LVDTFDKWQI LGRDVLSRLQ ASISIPEEVH
PPVVGVLDAP PSHIGLEHLP PPPEVPQFPL NLERLQALQD LVHRSLEAGY ISPWDGPGNN
PVFPVRKPNG AWRFVHDLRV TNALTKPIPA LSPGPPDLTA IPTHLPHIIC LDLKDAFFQI
PVEDRFRSYF AFTLPTPGGL QPHRRFAWRV LPQGFINSPA LFERALQEPL RQVSAAFSQS
LLVSYMDDIL YVSPTEEQRL QCYQTMAAHL RDLGFQVASE KTRQTPSPVP FLGQMVHERM
VTYQSLPTLQ ISSPISLHQL QTVLGDLQWV SRGTPTTRRP LQLLYSSLKG IDDPRAIIHL
SPEQQQGIAE LRQALSHNAR SRYNEQEPLL AYVHLTRAGS TLVLFQKGAQ FPLAYFQTPL
TDNQASPWGL LLLLGCQYLQ AQALSSYAKT ILKYYHNLPK TSLDNWIQSS EDPRVQELLQ
LWPQISSQGI QPPGPWKTLV TRAEVFLTPQ FSPEPIPAAL CLFSDGAARR GAYCLWKDHL
LDFQAVPAPE SAQKGELAGL LAGLAAAPPE PLNIWVDSKY LYSLLRTLVL GAWLQPDPVP
SYALLYKSLL RHPAIFVGHV RSHSSASHPI ASLNNYVDQL LPLETPEQWH KLTHCNSRAL
SRWPNPRISA WDPRSPATLC ETCQRLNPTG GGKMRTIQRG WAPNHIWQAD ITHYKYKQFT
YALHVFVDTY SGATHASAKR GLTTQTTIEG LLEAIVHLGR PKKLNTDQGA NYTSKTFVRF
CQQFGISLSH HVPYNPTSSG LVERTNGLLK LLLSKYHLDE PHLPMTQALS RALWTHNQIN
LLPILKTRWE LHHSPPLAVI SEGGETPKGS DKLFLYKLPG QNNRRWLGPL PALVEASGGA
LLATNPPVWV PWRLLKAFKC LKNDGPEDAP NRSSDG


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