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Protein

Gag-Pol polyprotein

Gene

pol

Organism
Baboon endogenous virus (strain M7)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Gag-Pol polyprotein: Plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag-Pol, or to Gag-Pol binding host factors. Interaction with HECT ubiquitin ligases probably links the viral protein to the host ESCRT pathway and facilitates release.By similarity
Matrix protein p15: Targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the pre-integration complex.By similarity
RNA-binding phosphoprotein p12: Constituent of the pre-integration complex (PIC) which tethers the latter to mitotic chromosomes. This allows the integration of the viral genome into the host DNA.By similarity
Capsid protein p30: Forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex.By similarity
Nucleocapsid protein p10-Pol: Involved in the packaging and encapsidation of two copies of the genome (By similarity). Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome (By similarity). This binding is dependent on genome dimerization (By similarity). Acts as a nucleic acid chaperone which is involved in rearrangement of nucleic acid secondary structures during gRNA retrotranscription (By similarity).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 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 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.Sequence analysis
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 the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. 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. The last step is viral DNA integration into host chromosome.By similarity

Miscellaneous

Gag-Pol polyprotein: This protein is translated as a gag-pol fusion protein by episodic readthrough of the gag protein termination codon. Readthrough of the terminator codon TAG occurs between the codons for 537-Asp and 539-Gly.By similarity
Nucleocapsid protein p10-Pol: Nucleocapsid protein p10-Pol released from Pol polyprotein (NC-pol) is a few amino acids shorter than the nucleocapsid protein p10 released from Gag polyprotein (NC-gag).By similarity
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.PROSITE-ProRule annotation

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+PROSITE-ProRule annotationNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation
  • Mg2+By similarityNote: Binds 1 magnesium ions for ribonuclease H (RNase H) activity.By similarity
  • Mg2+By similarityNote: Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.By similarity

Enzyme regulationi

Protease: Most efficiently inhibited by Amprenavir, which is able to block Gag-Pol processing in infected cells.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei565Protease; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi806Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi880Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi881Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1181Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1219Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1240Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1310MagnesiumPROSITE-ProRule annotation1
Metal bindingi1449Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1508Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri501 – 518CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1383 – 1421HHCC-typeBy similarityAdd BLAST39

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAspartyl protease, DNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein
Biological processDNA integration, DNA recombination, Host-virus interaction, 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:
Matrix protein p15
Short name:
MA
Alternative name(s):
pp12
Capsid protein p30
Short name:
CA
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
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:pol
OrganismiBaboon endogenous virus (strain M7)
Taxonomic identifieri11764 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeGammaretrovirusunclassified Gammaretrovirus
Virus hostiPapio (baboons) [TaxID: 9554]
Theropithecus gelada (Gelada baboon) [TaxID: 9565]
Proteomesi
  • UP000097294 Componenti: Genome
  • UP000007443 Componenti: Genome

Subcellular locationi

Gag-Pol polyprotein :
  • Virion By similarity
  • Host cell membrane By similarity; Lipid-anchor By similarity
  • Host late endosome membrane By similarity; Lipid-anchor By similarity
  • host multivesicular body By similarity
  • Note: These locations are probably linked to virus assembly sites.By similarity
Matrix protein p15 :
  • Virion By similarity
Capsid protein p30 :
  • Virion By similarity
Nucleocapsid protein p10-Pol :
  • Virion By similarity
Protease :
  • Virion By similarity
RNA-binding phosphoprotein p12 :
  • Host cytoplasm By similarity
  • Note: Localizes to the host cytoplasm early in infection and binds to the mitotic chromosomes later on.By similarity

GO - Cellular componenti

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host endosome, Host membrane, Membrane, Viral matrix protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedSequence analysis
ChainiPRO_00002597172 – 1727Gag-Pol polyproteinAdd BLAST1726
ChainiPRO_00004428742 – 129Matrix protein p15Add BLAST128
ChainiPRO_0000442875130 – 226RNA-binding phosphoprotein p12Add BLAST97
ChainiPRO_0000442876227 – 477Capsid protein p30Add BLAST251
ChainiPRO_0000442877478 – 533Nucleocapsid protein p10-PolAdd BLAST56
ChainiPRO_0000026123534 – 658ProteaseAdd BLAST125
ChainiPRO_0000026124659 – 1335Reverse transcriptase/ribonuclease HAdd BLAST677
ChainiPRO_00000261251336 – 1727IntegraseAdd BLAST392

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by hostSequence analysis1

Post-translational modificationi

Gag-Pol polyprotein: Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation.By similarity
RNA-binding phosphoprotein p12: Phosphorylated on serine residues.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei129 – 130Cleavage; by viral proteaseBy similarity2
Sitei226 – 227Cleavage; by viral proteaseBy similarity2
Sitei477 – 478Cleavage; by viral proteaseBy similarity2
Sitei533 – 534Cleavage; by viral proteaseBy similarity2
Sitei658 – 659Cleavage; by viral proteaseBy similarity2
Sitei1335 – 1336Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Interactioni

Subunit structurei

Capsid protein p30: Homohexamer; further associates as homomultimer (By similarity). Capsid protein p30: The virus core is composed of a lattice formed from hexagonal rings, each containing six capsid monomers (By similarity). Gag-Pol polyprotein: Interacts (via PPXY motif) with host NEDD4 (By similarity). Gag-Pol polyprotein: Interacts (via PSAP motif) with host TSG101 (By similarity). Gag-Pol polyprotein: Interacts (via LYPX(n)L motif) with host PDCD6IP (By similarity). Reverse transcriptase/ribonuclease H: The reverse transcriptase is a monomer (Potential). Reverse transcriptase/ribonuclease H: Interacts (via RNase domains) with host release factor ETF1; this interaction is essential for translational readthrough of amber codon between viral gag and pol genes, as well as for viral replication (By similarity). Integrase: Homodimer (By similarity).PROSITE-ProRule annotationBy similarity

Structurei

3D structure databases

ProteinModelPortaliP10272.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini560 – 630Peptidase A2PROSITE-ProRule annotationAdd BLAST71
Domaini736 – 929Reverse transcriptasePROSITE-ProRule annotationAdd BLAST194
Domaini1172 – 1318RNase HPROSITE-ProRule annotationAdd BLAST147
Domaini1438 – 1596Integrase catalyticPROSITE-ProRule annotationAdd BLAST159

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi109 – 112PTAP/PSAP motifBy similarity4
Motifi128 – 132LYPX(n)L motifBy similarity5
Motifi154 – 157PPXY motifBy similarity4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi93 – 205Pro-richPROSITE-ProRule annotationAdd BLAST113

Domaini

Gag-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. RNA-binding phosphoprotein p12 contains one L domain: a PPXY motif which potentially interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase. PPXY motif is essential for virus egress. Matrix protein p15 contains one L domain: a PTAP/PSAP motif, which potentially interacts with the UEV domain of TSG101. The junction between the matrix protein p15 and RNA-binding phosphoprotein p12 also contains one L domain: a LYPX(n)L motif which potentially interacts with PDCD6IP. Both PSAP and LYPX(n)L domains might play little to no role in budding and possibly drive residual virus release. contains.By similarity

Sequence similaritiesi

Belongs to the retroviral Pol polyprotein family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri501 – 518CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1383 – 1421HHCC-typeBy similarityAdd BLAST39

Keywords - Domaini

Zinc-finger

Phylogenomic databases

OrthoDBiVOG090000AJ.

Family and domain databases

CDDicd06095. RP_RTVL_H_like. 1 hit.
Gene3Di1.10.150.180. 1 hit.
1.10.375.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
InterProiView protein in InterPro
IPR001969. Aspartic_peptidase_AS.
IPR000840. G_retro_matrix.
IPR036946. G_retro_matrix_sf.
IPR003036. Gag_P30.
IPR001584. Integrase_cat-core.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom_sf.
IPR018061. Retropepsins.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR012337. RNaseH-like_sf.
IPR002156. RNaseH_domain.
IPR036397. RNaseH_sf.
IPR034145. RP_RTVL-H-like.
IPR000477. RT_dom.
IPR001878. Znf_CCHC.
IPR036875. Znf_CCHC_sf.
IPR015416. Znf_H2C2_histone_UAS-bd.
PfamiView protein in Pfam
PF01140. Gag_MA. 1 hit.
PF02093. Gag_p30. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF09337. zf-H2C2. 1 hit.
SMARTiView protein in SMART
SM00343. ZnF_C2HC. 1 hit.
SUPFAMiSSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50630. SSF50630. 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.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P10272-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGQTLTTPLS LTLTHFSDVR ARAHNLSVGV RKGRWQTFCS SEWPTLHVGW
60 70 80 90 100
PRDGTFDLSV ILQVKTKVMD PGPHGHPDQV AYIITWEDLV RNPPPWVKPF
110 120 130 140 150
LHTPSTSKST LLALEVPKNR TLDPPKPVLP DESQQDLLFQ DPLPHPPHNP
160 170 180 190 200
LLEPPPYNSP SPPVLSPVSP TTPSAPTPSS LVSSSTPPSS PAPPELTPRT
210 220 230 240 250
PPQTPRLRLR RAEGQDGPST WQSSLFPLRT VNRTIQYWPF SASDLYNWKT
260 270 280 290 300
HNPSFSQDPQ ALTSLIESIL LTHQPTWDDC QQLLQVLLTT EERQRVLLEA
310 320 330 340 350
RKNVPGPGGL PTQLPNEIDE GFPLTRPDWD YETAPGRESL RIYRQALLAG
360 370 380 390 400
LKGAGKRPTN LAKVRTITQG KDESPAAFME RLLEGFRMYT PFDPEAPEHK
410 420 430 440 450
ATVAMSFIDQ AALDIKGKLQ RLDGIQTHGL QELVREAEKV YNKRETPEER
460 470 480 490 500
EARLIKEQEE REDRRDRKRD KHLTKILAAV VTEKRAGKSG ETRRRPKVDK
510 520 530 540 550
DQCAYCKERG HWIKDCPKRP RDQKKPAPVL TLGEDSEQGC QGSGAPPEPR
560 570 580 590 600
LTLSVGGHPT TFLVDTGAQH SVLTKANGPL SSRTSWVQGA TGRKMHKWTN
610 620 630 640 650
RRTVNLGQGM VTHSFLVVPE CPYPLLGRDL LTKLGAQIHF SEAGAQVLDR
660 670 680 690 700
DGQPIQILTV SLQDEHRLFD IPVTTSLPDV WLQDFPQAWA ETGGLGRAKC
710 720 730 740 750
QAPIIIDLKP TAVPVSIKQY PMSLEAHMGI RQHIIKFLEL GVLRPCRSPW
760 770 780 790 800
NTPLLPVKKP GTQDYRPVQD LREINKRTVD IHPTVPNPYN LLSTLKPDYS
810 820 830 840 850
WYTVLDLKDA FFCLPLAPQS QELFAFEWKD PERGISGQLT WTRLPQGFKN
860 870 880 890 900
SPTLFDEALH RDLTDFRTQH PEVTLLQYVD DLLLAAPTKK ACTQGTRHLL
910 920 930 940 950
QELGEKGYRA SAKKAQICQT KVTYLGYILS EGKRWLTPGR IETVARIPPP
960 970 980 990 1000
RNPREVREFL GTAGFCRLWI PGFAELAAPL YALTKESTPF TWQTEHQLAF
1010 1020 1030 1040 1050
EALKKALLSA PALGLPDTSK PFTLFLDERQ GIAKGVLTQK LGPWKRPVAY
1060 1070 1080 1090 1100
LSKKLDPVAA GWPPCLRIMA ATAMLVKDSA KLTLGQPLTV ITPHTLEAIV
1110 1120 1130 1140 1150
RQPPDRWITN ARLTHYQALL LDTDRVQFGP PVTLNPATLL PVPENQPSPH
1160 1170 1180 1190 1200
DCRQVLAETH GTREDLKDQE LPDADHTWYT DGSSYLDSGT RRAGAAVVDG
1210 1220 1230 1240 1250
HNTIWAQSLP PGTSAQKAEL IALTKALELS KGKKANIYTD SRYAFATAHT
1260 1270 1280 1290 1300
HGSIYERRGL LTSEGKEIKN KAEIIALLKA LFLPQEVAII HCPGHQKGQD
1310 1320 1330 1340 1350
PVAVGNRQAD RVARQAAMAE VLTLATEPDN TSHITIEHTY TSEDQEEARA
1360 1370 1380 1390 1400
IGATENKDTR NWEKEGKIVL PQKEALAMIQ QMHAWTHLGN RKLKLLIEKT
1410 1420 1430 1440 1450
DFLIPRASTL IEQVTSACKV CQQVNAGATR VPAGKRTRGN RPGVYWEIDF
1460 1470 1480 1490 1500
TEVKPHYAGY KYLLVFVDTF SGWVEAFPTR QETAHIVAKK ILEEIFPRFG
1510 1520 1530 1540 1550
LPKVIGSDNG PAFVSQVSQG LARILGINWK LHCAYRPQSS GQVERMNRTI
1560 1570 1580 1590 1600
KETLTKLTLE TGLKDWRRLL SLALLRARNT PNRFGLTPYE ILYGGPPPLS
1610 1620 1630 1640 1650
TLLNSFSPSN SKTDLQARLK GLQAVQAQIW APLAELYRPG HSQTSHPFQV
1660 1670 1680 1690 1700
GDSVYVRRHR SQGLEPRWKG PYIVLLTTPT AIKVDGIATW IHASHAKAAP
1710 1720
GTPGPTSSGT WRLRRSEDPL KIRLSRT
Length:1,727
Mass (Da):192,980
Last modified:January 31, 2018 - v2
Checksum:iBAB4C7036AEAD476
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti125P → S in BAP91048 (PubMed:25463055).Curated1
Sequence conflicti496P → S in BAP91048 (PubMed:25463055).Curated1
Sequence conflicti500K → N in BAP91048 (PubMed:25463055).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10032 Genomic DNA. Translation: BAA89659.1.
AB979448 Genomic DNA. Translation: BAP91048.1.
PIRiJT0261. GNMVM7.
RefSeqiYP_009109689.1. NC_022517.1.

Genome annotation databases

GeneIDi22318531.
KEGGivg:22318531.

Keywords - Coding sequence diversityi

RNA suppression of termination

Similar proteinsi

Entry informationi

Entry nameiPOL_BAEVM
AccessioniPrimary (citable) accession number: P10272
Secondary accession number(s): A0A0A8IBU6, Q9IRA3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: January 31, 2018
Last modified: March 28, 2018
This is version 117 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome