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Protein

Gag-Pol polyprotein

Gene

pol

Organism
Maedi visna virus (strain 1514 / clone LV1-1KS1) (MVV) (Visna lentivirus)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

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.By similarity
Matrix protein p16: Targets the polyprotein to the plasma membrane.By similarity
Capsid protein p25: Forms the core that encapsulates the genomic RNA-nucleocapsid complex in the virion.By similarity
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.By similarity
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.PROSITE-ProRule annotation
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.PROSITE-ProRule annotation
Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.By similarity

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.PROSITE-ProRule annotation

Catalytic activityi

3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
dUTP + H2O = dUMP + diphosphate.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation

Cofactori

Mg2+PROSITE-ProRule annotationNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei464Protease; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi652Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi727Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi728Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi980Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1012Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1032Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1085MagnesiumPROSITE-ProRule annotation1
Metal bindingi1291Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1343Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1379Magnesium; catalytic; for integrase activityCurated1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri385 – 402CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri404 – 421CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1228 – 1269Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1447 – 1499Integrase-typePROSITE-ProRule annotationAdd BLAST53

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAspartyl protease, DNA-binding, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase
Biological processDNA integration, DNA recombination, Nucleotide metabolism, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Cleaved into the following 7 chains:
Alternative name(s):
Retropepsin (EC:3.4.23.-PROSITE-ProRule annotation)
Reverse transcriptase/ribonuclease H (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
RT
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:pol
OrganismiMaedi visna virus (strain 1514 / clone LV1-1KS1) (MVV) (Visna lentivirus)
Taxonomic identifieri11743 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusOvine/caprine lentivirus group
Virus hostiOvis aries (Sheep) [TaxID: 9940]

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004433621 – 143Matrix protein p16Add BLAST143
ChainiPRO_0000443363144 – 363Capsid protein p25Add BLAST220
ChainiPRO_0000443364364 – 442Nucleocapsid protein p14Add BLAST79
ChainiPRO_0000038861443 – 540ProteaseAdd BLAST98
ChainiPRO_0000038862541 – 1091Reverse transcriptase/ribonuclease HAdd BLAST551
ChainiPRO_00000388631092 – 1225Deoxyuridine 5'-triphosphate nucleotidohydrolaseAdd BLAST134
ChainiPRO_00000388641226 – 1506IntegraseAdd BLAST281

Post-translational modificationi

Gag-Pol polyprotein: Specific enzymatic cleavages by the viral protease yield mature proteins.Curated

Interactioni

Subunit structurei

Integrase: Homotetramer; further associates as a homohexadecamer.By similarity

Structurei

3D structure databases

ProteinModelPortaliP23426
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini459 – 530Peptidase A2PROSITE-ProRule annotationAdd BLAST72
Domaini587 – 776Reverse transcriptasePROSITE-ProRule annotationAdd BLAST190
Domaini971 – 1093RNase HPROSITE-ProRule annotationAdd BLAST123
Domaini1270 – 1430Integrase catalyticPROSITE-ProRule annotationAdd BLAST161

Sequence similaritiesi

Belongs to the retroviral Pol polyprotein family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri385 – 402CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri404 – 421CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1228 – 1269Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Repeat, Zinc-finger

Family and domain databases

CDDicd07557 trimeric_dUTPase, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
2.70.40.10, 1 hit
3.30.420.10, 2 hits
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR029054 dUTPase-like
IPR036157 dUTPase-like_sf
IPR033704 dUTPase_trimeric
IPR000721 Gag_p24
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010659 RVT_connect
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00692 dUTPase, 1 hit
PF00607 Gag_p24, 1 hit
PF02022 Integrase_Zn, 1 hit
PF00075 RNase_H, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF06815 RVT_connect, 1 hit
PF00098 zf-CCHC, 2 hits
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF46919 SSF46919, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF51283 SSF51283, 1 hit
SSF53098 SSF53098, 2 hits
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS50175 ASP_PROT_RETROV, 1 hit
PS00141 ASP_PROTEASE, 1 hit
PS50994 INTEGRASE, 1 hit
PS51027 INTEGRASE_DBD, 1 hit
PS50879 RNASE_H, 1 hit
PS50878 RT_POL, 1 hit
PS50158 ZF_CCHC, 2 hits
PS50876 ZF_INTEGRASE, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform Gag-Pol polyprotein (identifier: P23426-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAKQGSKEKK GYPELKEVIK ATCKIRVGPG KETLTEGNCL WALKTIDFIF
60 70 80 90 100
EDLKTEPWTI TKMYTVWDRL KGLTPEETSK REFASLQATL ACIMCSQMGM
110 120 130 140 150
KPETVQAAKG IISMKEGLQE NKEAKGEKVE QLYPNLEKHR EVYPIVNLQA
160 170 180 190 200
GGRSWKAVES VVFQQLQTVA MQHGLVSEDF ERQLAYYATT WTSKDILEVL
210 220 230 240 250
AMMPGNRAQK ELIQGKLNEE AERWVRQNPP GPNVLTVDQI MGVGQTNQQA
260 270 280 290 300
SQANMDQARQ ICRQWVITAL RSVRHMSHRP GNPMLVKQKN TESYEDFIAR
310 320 330 340 350
LLEAIDAEPV TDPIKTYLKV TLSYTNASTD CQKQMDRTLG TRVQQATVEE
360 370 380 390 400
KMQACRDVGS EGFKMQLLAQ ALRPQGKAGH KGVNQKCYNC GKPGHLARQC
410 420 430 440 450
RQGIICHHCG KRGHMQKDCR QKKQQGKQQE GATCGAVRAP YVVTEAPPKI
460 470 480 490 500
EIKVGTRWKK LLVDTGADKT IVTSHDMSGI PKGRIILQGI GGIIEGEKWE
510 520 530 540 550
QVHLQYKDKI IRGTIVVLAT SPVEVLGRDN MSELGIGLIM ANLEEKKIPI
560 570 580 590 600
TEVRLKEGCK GPHIAQWPLT QEKLEGLKEI VDRLEKEGKV GRAPPHWTCN
610 620 630 640 650
TPIFCIKKKS GKWRMLIDFR ELNKQTEDLA EAQLGLPHPG GLQRKKHVTI
660 670 680 690 700
LDIGDAYFTI PLYEPYRQYT CFTMLSPNNL GPCVRYYWKV LPQGWKLSPS
710 720 730 740 750
VYQFTMQKIL RGWIEEHPMI QFGIYMDDIY IGSDLGLEEH RGIVNELASY
760 770 780 790 800
IAQYGFMLPE DKRQEGYPAK WLGFELHPEK WKFQKHTLPE ITEGPITLNK
810 820 830 840 850
LQKLVGDLVW RQSLIGKSIP NILKLMEGDR ALQSERYIES IHVREWEACR
860 870 880 890 900
QKLKEMEGNY YDEEKDIYGQ LDWGNKAIEY IVFQEKGKPL WVNVVHSIKN
910 920 930 940 950
LSQAQQIIKA AQKLTQEVII RTGKIPWILL PGREEDWILE LQMGNINWMP
960 970 980 990 1000
SFWSCYKGSV RWKKRNVIAE VVSGPTYYTD GGKKNGRGSL GYIASTGEKF
1010 1020 1030 1040 1050
RIYEEGTNQQ LELRAIEEAC KQGPEKMNIV TDSRYAYEFM LRNWDEEVIR
1060 1070 1080 1090 1100
NPIQARIMEL MHNKEKIGVH WVPGHKGIPQ NEEIDRYISE IFLAKEGRGI
1110 1120 1130 1140 1150
LQKRAEDAGY DLICPQEISI PAGQVKRIAI DLKINLKKDQ WAMIGTKSSF
1160 1170 1180 1190 1200
ANKGVFVQGG IIDSGYQGTI QVVIYNSNNK EVVIPQGRKF AQLILMPLIH
1210 1220 1230 1240 1250
EELEPWGETR KTERGEQGFG STGMYWIENI PLAEEEHNKW HQDAVSLHLE
1260 1270 1280 1290 1300
FGIPRTAAED IVQQCDVCQE NKMPSTLRGS NKRGIDHWQV DYTHYEDKII
1310 1320 1330 1340 1350
LVWVETNSGL IYAERVKGET GQEFRVQTMK WYAMFAPKSL QSDNGPAFVA
1360 1370 1380 1390 1400
ESTQLLMKYL GIEHTTGIPW NPQSQALVER THQTLKNTLE KLIPMFNAFE
1410 1420 1430 1440 1450
SALAGTLITL NIKRKGGLGT SPMDIFIFNK EQQRIQQQSK SKQEKIRFCY
1460 1470 1480 1490 1500
YRTRKRGHPG EWQGPTQVLW GGDGAIVVKD RGTDRYLVIA NKDVKFIPPP

KEIQKE
Note: Produced by a -1 ribosomal frameshifting between gag and pol.By similarity
Length:1,506
Mass (Da):171,964
Last modified:February 28, 2018 - v2
Checksum:i2754F27EADA1204F
GO
Isoform Gag polyprotein (identifier: P23424-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P23424.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.By similarity
Length:442
Mass (Da):49,900
GO

Sequence cautioni

The sequence AAA17524 differs from that shown. Reason: Erroneous gene model prediction.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60609 Unassigned RNA Translation: AAA17524.1 Sequence problems.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Similar proteinsi

Entry informationi

Entry nameiPOL_VILV1
AccessioniPrimary (citable) accession number: P23426
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: February 28, 2018
Last modified: April 25, 2018
This is version 127 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health