UniProtKB - P35956 (POL_VILVK)
Gag-Pol polyprotein
pol
Functioni
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 similarityTargets the polyprotein to the plasma membrane.
By similarityForms the core that encapsulates the genomic RNA-nucleocapsid complex in the virion.
By similarityEncapsulates 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 similarityThe 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 annotationRT 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 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 annotationCatalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.
By similarityMiscellaneous
Catalytic activityi
- EC:3.6.1.23
- a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)PROSITE-ProRule annotationEC:2.7.7.49PROSITE-ProRule annotation EC:2.7.7.7PROSITE-ProRule annotation
- 3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. EC:3.1.13.2
- Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation EC:3.1.26.4
Cofactori
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 464 | Protease; shared with dimeric partnerPROSITE-ProRule annotation | 1 | |
Metal bindingi | 652 | Magnesium 1; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 727 | Magnesium 1; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 728 | Magnesium 1; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 980 | Magnesium 2; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1012 | Magnesium 2; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1032 | Magnesium 2; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1085 | Magnesium 2; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1237 | ZincPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1241 | ZincPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1265 | ZincPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1268 | ZincPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1291 | Magnesium 3; catalytic; for integrase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1343 | Magnesium 3; catalytic; for integrase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1379 | Magnesium 3; catalytic; for integrase activityCurated | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 385 – 402 | CCHC-type 1PROSITE-ProRule annotationAdd BLAST | 18 | |
Zinc fingeri | 404 – 421 | CCHC-type 2PROSITE-ProRule annotationAdd BLAST | 18 | |
Zinc fingeri | 1228 – 1269 | Integrase-typePROSITE-ProRule annotationAdd BLAST | 42 | |
DNA bindingi | 1447 – 1499 | Integrase-typePROSITE-ProRule annotationAdd BLAST | 53 |
GO - Molecular functioni
- aspartic-type endopeptidase activity Source: UniProtKB-KW
- DNA binding Source: UniProtKB-KW
- DNA-directed DNA polymerase activity Source: UniProtKB-EC
- dUTP diphosphatase activity Source: UniProtKB-EC
- exoribonuclease H activity Source: UniProtKB-EC
- RNA-directed DNA polymerase activity Source: UniProtKB-KW
- RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC
- zinc ion binding Source: InterPro
GO - Biological processi
- DNA integration Source: UniProtKB-KW
- DNA recombination Source: UniProtKB-KW
- establishment of integrated proviral latency Source: UniProtKB-KW
- nucleotide metabolic process Source: UniProtKB-KW
- viral entry into host cell Source: UniProtKB-KW
- viral genome integration into host DNA Source: UniProtKB-KW
Keywordsi
Molecular function | Aspartyl protease, DNA-binding, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase |
Biological process | DNA integration, DNA recombination, Nucleotide metabolism, Viral genome integration, Virus entry into host cell |
Ligand | Magnesium, Metal-binding, Zinc |
Protein family/group databases
MEROPSi | A02.006 |
Names & Taxonomyi
Protein namesi | Recommended name: Gag-Pol polyproteinCleaved into the following 7 chains: Alternative name(s): Retropepsin 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) |
Gene namesi | Name:pol |
Organismi | Maedi visna virus (strain KV1772) (MVV) (Visna lentivirus) |
Taxonomic identifieri | 36374 [NCBI] |
Taxonomic lineagei | Viruses › Riboviria › Pararnavirae › Artverviricota › Revtraviricetes › Ortervirales › Retroviridae › Orthoretrovirinae › Lentivirus › |
Virus hosti | Ovis aries (Sheep) [TaxID: 9940] |
Subcellular locationi
- Virion Curated
- Virion Curated
- Virion Curated
Keywords - Cellular componenti
Capsid protein, VirionPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000443369 | 1 – 1506 | Gag-Pol polyproteinAdd BLAST | 1506 | |
ChainiPRO_0000443370 | 1 – 143 | Matrix protein p16Add BLAST | 143 | |
ChainiPRO_0000443371 | 144 – 363 | Capsid protein p25Add BLAST | 220 | |
ChainiPRO_0000443372 | 364 – 442 | Nucleocapsid protein p14Add BLAST | 79 | |
ChainiPRO_0000038869 | 443 – 540 | ProteaseAdd BLAST | 98 | |
ChainiPRO_0000038870 | 541 – 1091 | Reverse transcriptase/ribonuclease HAdd BLAST | 551 | |
ChainiPRO_0000038871 | 1092 – 1225 | Deoxyuridine 5'-triphosphate nucleotidohydrolaseAdd BLAST | 134 | |
ChainiPRO_0000038872 | 1226 – 1506 | IntegraseAdd BLAST | 281 |
Post-translational modificationi
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 363 – 364 | Cleavage; by viral proteaseBy similarity | 2 |
Proteomic databases
PRIDEi | P35956 |
Interactioni
Subunit structurei
Structurei
Secondary structure
3D structure databases
SMRi | P35956 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P35956 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 459 – 530 | Peptidase A2PROSITE-ProRule annotationAdd BLAST | 72 | |
Domaini | 587 – 776 | Reverse transcriptasePROSITE-ProRule annotationAdd BLAST | 190 | |
Domaini | 971 – 1093 | RNase H type-1PROSITE-ProRule annotationAdd BLAST | 123 | |
Domaini | 1270 – 1430 | Integrase catalyticPROSITE-ProRule annotationAdd BLAST | 161 |
Sequence similaritiesi
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 385 – 402 | CCHC-type 1PROSITE-ProRule annotationAdd BLAST | 18 | |
Zinc fingeri | 404 – 421 | CCHC-type 2PROSITE-ProRule annotationAdd BLAST | 18 | |
Zinc fingeri | 1228 – 1269 | Integrase-typePROSITE-ProRule annotationAdd BLAST | 42 |
Keywords - Domaini
Repeat, Zinc-fingerFamily and domain databases
CDDi | cd07557, trimeric_dUTPase, 1 hit |
Gene3Di | 1.10.10.200, 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 3.30.70.270, 3 hits |
InterProi | View protein in InterPro IPR001969, Aspartic_peptidase_AS IPR043502, DNA/RNA_pol_sf IPR029054, dUTPase-like IPR036157, dUTPase-like_sf IPR033704, dUTPase_trimeric IPR045345, Gag_p24_C IPR000721, Gag_p24_N 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 IPR043128, Rev_trsase/Diguanyl_cyclase IPR012337, RNaseH-like_sf IPR002156, RNaseH_domain IPR036397, RNaseH_sf IPR000477, RT_dom IPR010659, RVT_connect IPR001878, Znf_CCHC IPR036875, Znf_CCHC_sf |
Pfami | View protein in Pfam PF00692, dUTPase, 1 hit PF00607, Gag_p24, 1 hit PF19317, Gag_p24_C, 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 |
SMARTi | View protein in SMART SM00343, ZnF_C2HC, 2 hits |
SUPFAMi | SSF46919, SSF46919, 1 hit SSF47943, SSF47943, 1 hit SSF50122, SSF50122, 1 hit SSF50630, SSF50630, 1 hit SSF51283, SSF51283, 1 hit SSF53098, SSF53098, 2 hits SSF56672, SSF56672, 1 hit SSF57756, SSF57756, 1 hit |
PROSITEi | View 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, 1 hit PS50878, RT_POL, 1 hit PS50158, ZF_CCHC, 2 hits PS50876, ZF_INTEGRASE, 1 hit |
s (2)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry describes 2 produced by isoformsiribosomal frameshifting. AlignAdd to basketThis isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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 IISMKEGLHE 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 ICLQWVITAL RSVRHMSHRP GNPMLVKQKN TESYEDFIAR
310 320 330 340 350
LLEAIDAEPV TDPIKTYLKV TLSYTNASTD CQKQMDRTLG TRVQQATVEE
360 370 380 390 400
KMQACRDVGS EGFKMQLLAQ ALRPQGKAGQ 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 MRELGIGLIM ANLEEKKIPS
560 570 580 590 600
TRVRLKEGCK GPHIAQWPLT QEKLEGLKEI VDRLEKEGKV GRAPPHWTCN
610 620 630 640 650
TPIFCIKKKS GKWRMLIDFR ELNKQTEDLA EAQLGLPHPG GLQRKKHVTI
660 670 680 690 700
LDIGDAYFTI PLYEPYRQYT CFTMLSPNNL GPCVRYYWKV LPQGWKLSPA
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 VVPGPTYYTD GGKKNGRGSL GYITSTGEKF
1010 1020 1030 1040 1050
RIHEEGTNQQ LELRAIEEAC KQGPEKMNIV TDSRYAYEFM LRNWDEEVIR
1060 1070 1080 1090 1100
NPIQARIMEL VHNKEKIGVH 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
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Sequence cautioni
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L06906 Genomic RNA Translation: AAA48359.1 Sequence problems. S55323 Genomic DNA Translation: AAB25460.1 Sequence problems. |
Keywords - Coding sequence diversityi
Ribosomal frameshiftingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L06906 Genomic RNA Translation: AAA48359.1 Sequence problems. S55323 Genomic DNA Translation: AAB25460.1 Sequence problems. |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3HPG | X-ray | 3.28 | A/B/C/D/E/F | 1228-1445 | [»] | |
3HPH | X-ray | 2.64 | A/B/C/D | 1228-1445 | [»] | |
5LLJ | X-ray | 1.78 | A/B | 1444-1501 | [»] | |
5M0Q | electron microscopy | 4.91 | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P | 1228-1506 | [»] | |
5M0R | electron microscopy | 8.20 | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P | 1228-1506 | [»] | |
5T3A | X-ray | 2.50 | A | 1285-1506 | [»] | |
SMRi | P35956 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein family/group databases
MEROPSi | A02.006 |
Proteomic databases
PRIDEi | P35956 |
Miscellaneous databases
EvolutionaryTracei | P35956 |
Family and domain databases
CDDi | cd07557, trimeric_dUTPase, 1 hit |
Gene3Di | 1.10.10.200, 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 3.30.70.270, 3 hits |
InterProi | View protein in InterPro IPR001969, Aspartic_peptidase_AS IPR043502, DNA/RNA_pol_sf IPR029054, dUTPase-like IPR036157, dUTPase-like_sf IPR033704, dUTPase_trimeric IPR045345, Gag_p24_C IPR000721, Gag_p24_N 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 IPR043128, Rev_trsase/Diguanyl_cyclase IPR012337, RNaseH-like_sf IPR002156, RNaseH_domain IPR036397, RNaseH_sf IPR000477, RT_dom IPR010659, RVT_connect IPR001878, Znf_CCHC IPR036875, Znf_CCHC_sf |
Pfami | View protein in Pfam PF00692, dUTPase, 1 hit PF00607, Gag_p24, 1 hit PF19317, Gag_p24_C, 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 |
SMARTi | View protein in SMART SM00343, ZnF_C2HC, 2 hits |
SUPFAMi | SSF46919, SSF46919, 1 hit SSF47943, SSF47943, 1 hit SSF50122, SSF50122, 1 hit SSF50630, SSF50630, 1 hit SSF51283, SSF51283, 1 hit SSF53098, SSF53098, 2 hits SSF56672, SSF56672, 1 hit SSF57756, SSF57756, 1 hit |
PROSITEi | View 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, 1 hit PS50878, RT_POL, 1 hit PS50158, ZF_CCHC, 2 hits PS50876, ZF_INTEGRASE, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | POL_VILVK | |
Accessioni | P35956Primary (citable) accession number: P35956 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 1, 1994 |
Last sequence update: | February 28, 2018 | |
Last modified: | February 23, 2022 | |
This is version 144 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Viral Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structureDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families