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Gag-Pol polyprotein [Cleaved into: Matrix protein p16; Capsid protein p25; Nucleocapsid protein p14; Protease (Retropepsin) (EC 3.4.23.-); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (Exoribonuclease H) (EC 3.1.13.2); Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (EC 3.6.1.23); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]

 POL_VILV1               Reviewed;        1506 AA.
P23426;
01-NOV-1991, integrated into UniProtKB/Swiss-Prot.
28-FEB-2018, sequence version 2.
12-SEP-2018, entry version 130.
RecName: Full=Gag-Pol polyprotein;
Contains:
RecName: Full=Matrix protein p16;
Contains:
RecName: Full=Capsid protein p25;
Contains:
RecName: Full=Nucleocapsid protein p14;
Contains:
RecName: Full=Protease;
AltName: Full=Retropepsin;
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};
AltName: Full=Exoribonuclease H;
EC=3.1.13.2;
Contains:
RecName: Full=Deoxyuridine 5'-triphosphate nucleotidohydrolase;
Short=dUTPase;
EC=3.6.1.23;
Contains:
RecName: Full=Integrase;
Short=IN;
EC=2.7.7.- {ECO:0000250|UniProtKB:P03370};
EC=3.1.-.- {ECO:0000250|UniProtKB:P03370};
Name=pol;
Maedi visna virus (strain 1514 / clone LV1-1KS1) (MVV) (Visna
lentivirus).
Viruses; Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
NCBI_TaxID=11743;
NCBI_TaxID=9940; Ovis aries (Sheep).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=1847257; DOI=10.1016/0042-6822(91)90488-W;
Staskus K.A., Retzel E.F., Lewis E.D., Wietgrefe S.W., Silsby J.L.,
Cyr S., Rank J.M., Haase A.T., Fast D., Geiser P.T., Harty J.T.,
Kong S.H., Cook R., Lahti C.J., Neufeld T.P., Porter T.E., Shoop E.,
Zachow K.R.;
"Isolation of replication-competent molecular clones of visna virus.";
Virology 181:228-240(1991).
-!- FUNCTION: Gag-Pol polyprotein: Mediates, with Gag polyprotein, the
essential events in virion assembly, including binding the plasma
membrane, making the protein-protein interactions necessary to
create spherical particles, recruiting the viral Env proteins, and
packaging the genomic RNA via direct interactions with the RNA
packaging sequence. {ECO:0000250|UniProtKB:P04585}.
-!- FUNCTION: Matrix protein p16: Targets the polyprotein to the
plasma membrane. {ECO:0000250|UniProtKB:P12497}.
-!- FUNCTION: Capsid protein p25: Forms the core that encapsulates the
genomic RNA-nucleocapsid complex in the virion.
{ECO:0000250|UniProtKB:P04585}.
-!- FUNCTION: Nucleocapsid protein p14: Encapsulates and protects
viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs
through its zinc fingers. Acts as a nucleic acid chaperone which
is involved in rearrangement of nucleic acid secondary structure
during gRNA retrotranscription. Also facilitates template switch
leading to recombination. {ECO:0000250|UniProtKB:P04585}.
-!- 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 dimeric 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-Trp 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 perfom 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 perfom
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
primers. 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:0000255|PROSITE-ProRule:PRU00405}.
-!- FUNCTION: Integrase: Catalyzes viral DNA integration into the host
chromosome, by performing a series of DNA cutting and joining
reactions. {ECO:0000250|UniProtKB:P03370}.
-!- CATALYTIC ACTIVITY: 3'-end directed exonucleolytic cleavage of
viral RNA-DNA hybrid.
-!- CATALYTIC ACTIVITY: dUTP + H(2)O = dUMP + diphosphate.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00405}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester. {ECO:0000255|PROSITE-ProRule:PRU00408}.
-!- 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: Integrase: Homotetramer; further associates as a
homohexadecamer. {ECO:0000250|UniProtKB:P35956}.
-!- SUBCELLULAR LOCATION: Matrix protein p16: Virion {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Capsid protein p25: Virion {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Nucleocapsid protein p14: Virion
{ECO:0000305}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=2;
Name=Gag-Pol polyprotein;
IsoId=P23426-1; Sequence=Displayed;
Note=Produced by a -1 ribosomal frameshifting between gag and
pol. {ECO:0000250|UniProtKB:P35956};
Name=Gag polyprotein;
IsoId=P23424-1; Sequence=External;
Note=Produced by conventional translation.
{ECO:0000250|UniProtKB:P35956};
-!- PTM: Gag-Pol polyprotein: Specific enzymatic cleavages by the
viral protease yield mature proteins. {ECO:0000305}.
-!- 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 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=AAA17524.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; M60609; AAA17524.1; ALT_SEQ; Unassigned_RNA.
ProteinModelPortal; P23426; -.
PRIDE; P23426; -.
GO; GO:0019028; C:viral capsid; 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:0004170; F:dUTP diphosphatase activity; IEA:UniProtKB-EC.
GO; GO:0004533; F:exoribonuclease H 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: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:0009117; P:nucleotide metabolic process; 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.
CDD; cd07557; trimeric_dUTPase; 1.
Gene3D; 1.10.10.200; -; 1.
Gene3D; 1.10.1200.30; -; 1.
Gene3D; 1.10.375.10; -; 1.
Gene3D; 2.30.30.10; -; 1.
Gene3D; 2.40.70.10; -; 1.
Gene3D; 2.70.40.10; -; 1.
Gene3D; 3.30.420.10; -; 2.
InterPro; IPR001969; Aspartic_peptidase_AS.
InterPro; IPR029054; dUTPase-like.
InterPro; IPR036157; dUTPase-like_sf.
InterPro; IPR033704; dUTPase_trimeric.
InterPro; IPR000721; Gag_p24.
InterPro; IPR017856; Integrase-like_N.
InterPro; IPR036862; Integrase_C_dom_sf_retrovir.
InterPro; IPR001037; Integrase_C_retrovir.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR003308; Integrase_Zn-bd_dom_N.
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; IPR012337; RNaseH-like_sf.
InterPro; IPR002156; RNaseH_domain.
InterPro; IPR036397; RNaseH_sf.
InterPro; IPR000477; RT_dom.
InterPro; IPR010659; RVT_connect.
InterPro; IPR001878; Znf_CCHC.
InterPro; IPR036875; Znf_CCHC_sf.
Pfam; PF00692; dUTPase; 1.
Pfam; PF00607; Gag_p24; 1.
Pfam; PF02022; Integrase_Zn; 1.
Pfam; PF00075; RNase_H; 1.
Pfam; PF00665; rve; 1.
Pfam; PF00077; RVP; 1.
Pfam; PF00078; RVT_1; 1.
Pfam; PF06815; RVT_connect; 1.
Pfam; PF00098; zf-CCHC; 2.
SMART; SM00343; ZnF_C2HC; 2.
SUPFAM; SSF46919; SSF46919; 1.
SUPFAM; SSF47943; SSF47943; 1.
SUPFAM; SSF50122; SSF50122; 1.
SUPFAM; SSF50630; SSF50630; 1.
SUPFAM; SSF51283; SSF51283; 1.
SUPFAM; SSF53098; SSF53098; 2.
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; 2.
PROSITE; PS50876; ZF_INTEGRASE; 1.
3: Inferred from homology;
Aspartyl protease; Capsid protein; DNA integration; DNA recombination;
DNA-binding; Endonuclease; Hydrolase; Magnesium; Metal-binding;
Multifunctional enzyme; Nuclease; Nucleotide metabolism;
Nucleotidyltransferase; Protease; Repeat; Ribosomal frameshifting;
RNA-directed DNA polymerase; Transferase; Viral genome integration;
Virion; Virus entry into host cell; Zinc; Zinc-finger.
CHAIN 1 143 Matrix protein p16.
/FTId=PRO_0000443362.
CHAIN 144 363 Capsid protein p25.
/FTId=PRO_0000443363.
CHAIN 364 442 Nucleocapsid protein p14.
/FTId=PRO_0000443364.
CHAIN 443 540 Protease.
/FTId=PRO_0000038861.
CHAIN 541 1091 Reverse transcriptase/ribonuclease H.
/FTId=PRO_0000038862.
CHAIN 1092 1225 Deoxyuridine 5'-triphosphate
nucleotidohydrolase.
/FTId=PRO_0000038863.
CHAIN 1226 1506 Integrase.
/FTId=PRO_0000038864.
DOMAIN 459 530 Peptidase A2. {ECO:0000255|PROSITE-
ProRule:PRU00275}.
DOMAIN 587 776 Reverse transcriptase.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
DOMAIN 971 1093 RNase H. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
DOMAIN 1270 1430 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
ZN_FING 385 402 CCHC-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 404 421 CCHC-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 1228 1269 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00450}.
DNA_BIND 1447 1499 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00506}.
ACT_SITE 464 464 Protease; shared with dimeric partner.
{ECO:0000255|PROSITE-ProRule:PRU00275}.
METAL 652 652 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
METAL 727 727 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
METAL 728 728 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
METAL 980 980 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1012 1012 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1032 1032 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1085 1085 Magnesium. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 1291 1291 Magnesium; catalytic; for integrase
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1343 1343 Magnesium; catalytic; for integrase
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1379 1379 Magnesium; catalytic; for integrase
activity. {ECO:0000305}.
SEQUENCE 1506 AA; 171964 MW; 2754F27EADA1204F CRC64;
MAKQGSKEKK GYPELKEVIK ATCKIRVGPG KETLTEGNCL WALKTIDFIF EDLKTEPWTI
TKMYTVWDRL KGLTPEETSK REFASLQATL ACIMCSQMGM KPETVQAAKG IISMKEGLQE
NKEAKGEKVE QLYPNLEKHR EVYPIVNLQA GGRSWKAVES VVFQQLQTVA MQHGLVSEDF
ERQLAYYATT WTSKDILEVL AMMPGNRAQK ELIQGKLNEE AERWVRQNPP GPNVLTVDQI
MGVGQTNQQA SQANMDQARQ ICRQWVITAL RSVRHMSHRP GNPMLVKQKN TESYEDFIAR
LLEAIDAEPV TDPIKTYLKV TLSYTNASTD CQKQMDRTLG TRVQQATVEE KMQACRDVGS
EGFKMQLLAQ ALRPQGKAGH KGVNQKCYNC GKPGHLARQC RQGIICHHCG KRGHMQKDCR
QKKQQGKQQE GATCGAVRAP YVVTEAPPKI EIKVGTRWKK LLVDTGADKT IVTSHDMSGI
PKGRIILQGI GGIIEGEKWE QVHLQYKDKI IRGTIVVLAT SPVEVLGRDN MSELGIGLIM
ANLEEKKIPI TEVRLKEGCK GPHIAQWPLT QEKLEGLKEI VDRLEKEGKV GRAPPHWTCN
TPIFCIKKKS GKWRMLIDFR ELNKQTEDLA EAQLGLPHPG GLQRKKHVTI LDIGDAYFTI
PLYEPYRQYT CFTMLSPNNL GPCVRYYWKV LPQGWKLSPS VYQFTMQKIL RGWIEEHPMI
QFGIYMDDIY IGSDLGLEEH RGIVNELASY IAQYGFMLPE DKRQEGYPAK WLGFELHPEK
WKFQKHTLPE ITEGPITLNK LQKLVGDLVW RQSLIGKSIP NILKLMEGDR ALQSERYIES
IHVREWEACR QKLKEMEGNY YDEEKDIYGQ LDWGNKAIEY IVFQEKGKPL WVNVVHSIKN
LSQAQQIIKA AQKLTQEVII RTGKIPWILL PGREEDWILE LQMGNINWMP SFWSCYKGSV
RWKKRNVIAE VVSGPTYYTD GGKKNGRGSL GYIASTGEKF RIYEEGTNQQ LELRAIEEAC
KQGPEKMNIV TDSRYAYEFM LRNWDEEVIR NPIQARIMEL MHNKEKIGVH WVPGHKGIPQ
NEEIDRYISE IFLAKEGRGI LQKRAEDAGY DLICPQEISI PAGQVKRIAI DLKINLKKDQ
WAMIGTKSSF ANKGVFVQGG IIDSGYQGTI QVVIYNSNNK EVVIPQGRKF AQLILMPLIH
EELEPWGETR KTERGEQGFG STGMYWIENI PLAEEEHNKW HQDAVSLHLE FGIPRTAAED
IVQQCDVCQE NKMPSTLRGS NKRGIDHWQV DYTHYEDKII LVWVETNSGL IYAERVKGET
GQEFRVQTMK WYAMFAPKSL QSDNGPAFVA ESTQLLMKYL GIEHTTGIPW NPQSQALVER
THQTLKNTLE KLIPMFNAFE SALAGTLITL NIKRKGGLGT SPMDIFIFNK EQQRIQQQSK
SKQEKIRFCY YRTRKRGHPG EWQGPTQVLW GGDGAIVVKD RGTDRYLVIA NKDVKFIPPP
KEIQKE


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