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Protein

Gag-Pro-Pol polyprotein

Gene

gag-pro-pol

Organism
Mouse mammary tumor virus (strain C3H) (MMTV)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Matrix protein p10: Matrix protein.Curated
Nucleocapsid protein p14: Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs.Curated
Capsid protein p27: capsid protein.Curated
NC-dUTPase has dUTPase activity, thereby preventing incorporation of uracil into DNA.1 Publication
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 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.1 Publication1 Publication

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.PROSITE-ProRule annotation

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation
dUTP + H2O = dUMP + diphosphate.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Mg2+PROSITE-ProRule annotationNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation
  • Mg2+Note: Magnesium ions are required for NC-dUTPase activity.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei771Protease; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi970Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1045Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1046Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1316Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1346Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1366Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1429MagnesiumPROSITE-ProRule annotation1
Metal bindingi1501Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1558Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1594Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri525 – 542CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri552 – 569CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1436 – 1477Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1653 – 1702Integrase-typePROSITE-ProRule annotationAdd BLAST50

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, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pro-Pol polyprotein
Cleaved into the following 10 chains:
Nucleocapsid protein-dUTPase (EC:3.6.1.231 Publication)
Short name:
NC-dUTPase
Protease (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
Integrase (EC:2.7.7.-1 Publication, EC:3.1.-.-1 Publication)
Short name:
IN
Gene namesi
Name:gag-pro-pol
OrganismiMouse mammary tumor virus (strain C3H) (MMTV)
Taxonomic identifieri11759 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeBetaretrovirus
Virus hostiMus musculus (Mouse) [TaxID: 10090]
Proteomesi
  • UP000006540 Componenti: Genome

Subcellular locationi

Matrix protein p10 :
  • Virion By similarity
Capsid protein p27 :
  • Virion By similarity
Nucleocapsid protein-dUTPase :
  • Virion By similarity

GO - Cellular componenti

Keywords - Cellular componenti

Capsid protein, Viral matrix protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostSequence analysis
ChainiPRO_00001254932 – 1755Gag-Pro-Pol polyproteinAdd BLAST1754
ChainiPRO_00004036122 – 99Matrix protein p10Add BLAST98
ChainiPRO_0000403613100 – 195Phosphorylated protein pp21Add BLAST96
ChainiPRO_0000403614196 – 228Protein p3Add BLAST33
ChainiPRO_0000403615229 – 254Protein p8Add BLAST26
ChainiPRO_0000403616255 – 269Protein nAdd BLAST15
ChainiPRO_0000403617270 – 496Capsid protein p27Add BLAST227
ChainiPRO_0000403618497 – 745Nucleocapsid protein-dUTPaseAdd BLAST249
ChainiPRO_0000403619746 – 860ProteaseAdd BLAST115
ChainiPRO_0000403620861 – 1437Reverse transcriptase/ribonuclease HAdd BLAST577
ChainiPRO_00004036211438 – 1755IntegraseAdd BLAST318

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by host1 Publication1

Post-translational modificationi

Protease: Released by autocatalytic processing.By similarity
Gag-Pro-Pol polyprotein: Specific enzymatic cleavages in vivo yield mature proteins.1 Publication
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.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei99 – 100Cleavage; by viral protease1 Publication2
Sitei195 – 196Cleavage; by viral protease1 Publication2
Sitei228 – 229Cleavage; by viral protease1 Publication2
Sitei254 – 255Cleavage; by viral protease1 Publication2
Sitei269 – 270Cleavage; by viral protease1 Publication2
Sitei496 – 497Cleavage; by viral protease1 Publication2
Sitei745 – 746Cleavage; by viral protease1 Publication2
Sitei1437 – 1438Cleavage; by viral protease1 Publication2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Interactioni

Subunit structurei

Matrix protein p10: Homodimer; when myristoylated (By similarity). Protease: Homodimer (By similarity). Integrase: Homooctamer (PubMed:28458055). NC-dUTPase is a homotrimer (PubMed:8091672).1 PublicationBy similarity1 Publication

Structurei

3D structure databases

ProteinModelPortaliP11283
SMRiP11283
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini766 – 841Peptidase A2PROSITE-ProRule annotationAdd BLAST76
Domaini905 – 1093Reverse transcriptasePROSITE-ProRule annotationAdd BLAST189
Domaini1307 – 1435RNase HPROSITE-ProRule annotationAdd BLAST129
Domaini1490 – 1647Integrase catalyticPROSITE-ProRule annotationAdd BLAST158

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi305 – 308PTAP/PSAP motifCurated4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi278 – 281Poly-Asp4
Compositional biasi716 – 719Poly-Leu4

Domaini

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. Gag-p27 contains one L domain: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri525 – 542CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri552 – 569CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1436 – 1477Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

OrthoDBiVOG09000135

Family and domain databases

CDDicd05482 HIV_retropepsin_like, 1 hit
cd07557 trimeric_dUTPase, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.490, 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
IPR003322 B_retro_matrix
IPR038124 B_retro_matrix_sf
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
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010661 RVT_thumb
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00692 dUTPase, 1 hit
PF02337 Gag_p10, 1 hit
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_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
PF06817 RVT_thumb, 1 hit
PF00098 zf-CCHC, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD004265 B_retro_matrix_N, 1 hit
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF46919 SSF46919, 1 hit
SSF47836 SSF47836, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF51283 SSF51283, 1 hit
SSF53098 SSF53098, 2 hits
SSF57756 SSF57756, 2 hits
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, 1 hit
PS50876 ZF_INTEGRASE, 1 hit

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform Gag-Pro-Pol polyprotein (identifier: P11283-1) [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
MGVSGSKGQK LFVSVLQRLL SERGLHVKES SAIEFYQFLI KVSPWFPEEG
60 70 80 90 100
GLNLQDWKRV GREMKKYAAE HGTDSIPKQA YPIWLQLREI LTEQSDLVLL
110 120 130 140 150
SAEAKSVTEE ELEEGLTGLL SASSQEKTYG TRGTAYAEID TEVDKLSEHI
160 170 180 190 200
YDEPYEEKEK ADKNEEKDHV RKVKKIVQRK ENSEHKRKEK DQKAFLATDW
210 220 230 240 250
NNDDLSPEDW DDLEEQAAHY HDDDELILPV KRKVDKKKPL ALRRKPLPPV
260 270 280 290 300
GFAGAMAEAR EKGDLTFTFP VVFMGESDDD DTPVWEPLPL KTLKELQSAV
310 320 330 340 350
RTMGPSAPYT LQVVDMVASQ WLTPSDWHQT ARATLSPGDY VLWRTEYEEK
360 370 380 390 400
SKETVQKTAG KRKGKVSLDM LLGTGQFLSP SSQIKLSKDV LKDVTTNAVL
410 420 430 440 450
AWRAIPPPGV KKTVLAGLKQ GNEESYETFI SRLEEAVYRM MPRGEGSDIL
460 470 480 490 500
IKQLAWENAN SLCQDLIRPM RKTGTMQDYI RACLDASPAV VQGMAYAAAM
510 520 530 540 550
RGQKYSTFVK QTYGGGKGGQ GSEGPVCFSC GKTGHIKRDC KEEKGSKRAP
560 570 580 590 600
PGLCPRCKKG YHWKSECKSK FDKDGNPLPP LETNAENSKN LVKGQSPSPT
610 620 630 640 650
QKGDKGKDSG LNPEAPPFTI HDLPRGTPGS AGLDLSSQKD LILSLEDGVS
660 670 680 690 700
LVPTLVKGTL PEGTTGLIIG RSSNYKKGLE VLPGVIDSDF QGEIKVMVKA
710 720 730 740 750
AKNAVIIHKG ERIAQLLLLP YLKLPNPIIK EERGSEGFGS TSHVHWVQEI
760 770 780 790 800
SDSRPMLHIS LNGRRFLGLL DTGADKTCIA GRDWPANWPI HQTESSLQGL
810 820 830 840 850
GMACGVARSS QPLRWQHEDK SGIIHPFVIP TLPFTLWGRD IMKEIKVRLM
860 870 880 890 900
TDSPDDSQDL MIGAIESNLF ADQISWKSDQ PVWLNQWPLK QEKLQALQQL
910 920 930 940 950
VTEQLQLGHL EESNSPWNTP VFVIKKKSGK WRLLQDLRAV NATMHDMGAL
960 970 980 990 1000
QPGLPSPVAV PKGWEIIIID LQDCFFNIKL HPEDCKRFAF SVPSPNFKRP
1010 1020 1030 1040 1050
YQRFQWKVLP QGMKNSPTLC QKFVDKAILT VRDKYQDSYI VHYMDDILLA
1060 1070 1080 1090 1100
HPSRSIVDEI LTSMIQALNK HGLVVSTEKI QKYDNLKYLG THIQGDAVSY
1110 1120 1130 1140 1150
QKLQIRTDKL RTLNDFQKLL GNINWIRPFL KLTTGELKPL FEILNGDSNP
1160 1170 1180 1190 1200
ISIRKLTPEA CKALQLVNER LSIARVKRLD LSRPWSLCIL KTEYTPTACL
1210 1220 1230 1240 1250
WQNGVLEWIH LPHISPKVIT PYDIFCTQLI IKGRHRSKEL FSKDPDYIVV
1260 1270 1280 1290 1300
PYTKVQFDLL LQEKEDWPIS LLGFLGEVHF HLPKDPLLTF TLQTAIIFPH
1310 1320 1330 1340 1350
MTSTTPLEKG IVIFTDGSAN GRSVTYIQGR EPIIKENTQN TAQQAEIVAV
1360 1370 1380 1390 1400
ITAFEEVSQS FNLYTDSKYV TGLFPEIETA TLSPRTKIYT ELRHLQRLIH
1410 1420 1430 1440 1450
KRQEKFYIGH IRGHTGLPGP LAQGNAYADS LTRILTALES AQESHALHHQ
1460 1470 1480 1490 1500
NAAALRFQFH ITREQAREIV KLCPNCPDWG HAPQLGVNPR GLKPRVLWQM
1510 1520 1530 1540 1550
DVTHVSEFGK LKYVHVTVDT YSHFTFATAR TGEATKDVLQ HLAQSFAYMG
1560 1570 1580 1590 1600
FPQKIKTDNA PAYVSRSIQE FLARWKISHV TGIPYNPQGQ AIVERTHQNI
1610 1620 1630 1640 1650
KAQLNKLQKA GKYYTPHHLL AHALFVLNHV NMDNQGHTAA ERHWGPISAD
1660 1670 1680 1690 1700
PKPMVMWKDL LAGSWKGPDV LITAGRGYAC VFPQDAETPI WVPDRFIRPF
1710 1720 1730 1740 1750
TERKEATPTP GTAEKTPPRD EKDQQKSPED ESSPHQREDG LATSAGVNLR

SGGGS
Note: Produced by -1 ribosomal frameshiftings between gag-pro and pro-pol.2 Publications
Length:1,755
Mass (Da):197,329
Last modified:January 11, 2011 - v2
Checksum:i0E99A2ADD96823A4
GO
Isoform Gag-Pro polyprotein (identifier: Q9IZT2-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry Q9IZT2.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by -1 ribosomal frameshifting between gag-pro.2 Publications
Length:860
Mass (Da):95,593
GO
Isoform Gag polyprotein (identifier: P11284-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P11284.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.2 Publications
Length:591
Mass (Da):66,351
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti857 – 860SQDL → FTGF in AAA66625 (PubMed:3035577).Curated4
Sequence conflicti867S → T in AAA66625 (PubMed:3035577).Curated1
Sequence conflicti952P → L in AAA66625 (PubMed:3035577).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti523E → K. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF228552 Genomic DNA Translation: AAF31474.1
M16766 Genomic RNA Translation: AAA66623.1
M16766 Genomic RNA Translation: AAA66625.1
PIRiB29029

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Similar proteinsi

Entry informationi

Entry nameiPOL_MMTVC
AccessioniPrimary (citable) accession number: P11283
Secondary accession number(s): Q9IZT3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: January 11, 2011
Last modified: March 28, 2018
This is version 96 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, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health