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P11283 (POL_MMTVC) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Gag-Pro-Pol polyprotein
Gene names
Name:gag-pro-pol
OrganismMouse mammary tumor virus (strain C3H) (MMTV) [Reference proteome]
Taxonomic identifier11759 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeBetaretrovirus
Virus hostMus musculus (Mouse) [TaxID: 10090]

Protein attributes

Sequence length1755 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Matrix protein p10: Matrix protein By similarity.

Nucleocapsid protein p14: Nucleocapsid protein. Binds to single-stranded DNA By similarity.

Capsid protein p27: capsid protein By similarity.

NC-dUTPase has dUTPase activity, thereby preventing incorporation of uracil into DNA.

The aspartyl protease mediates proteolytic cleavages of Gag, Gag-Pro and Gag-Pro-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 By similarity.

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 By similarity.

Catalytic activity

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Endonucleolytic cleavage to 5'-phosphomonoester.

Cofactor

RT polymerase domain: Binds 2 magnesium ions By similarity.

Magnesium ions for NC-dUTPase.

Subunit structure

NC-dUTPase is a homotrimer. Ref.5

Subcellular location

Matrix protein p10: Virion Potential.

Capsid protein p27: Virion Potential.

Nucleocapsid protein-dUTPase: Virion Potential.

Post-translational modification

Specific enzymatic cleavages in vivo yield mature proteins.

p10 is myristoylated.

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 By similarity.

Sequence similarities

Contains 2 CCHC-type zinc fingers.

Contains 1 integrase catalytic domain.

Contains 1 integrase-type DNA-binding domain.

Contains 1 integrase-type zinc finger.

Contains 1 peptidase A2 domain.

Contains 1 reverse transcriptase domain.

Contains 1 RNase H domain.

Ontologies

Keywords
   Biological processDNA integration
DNA recombination
Viral genome integration
Virus entry into host cell
   Cellular componentCapsid protein
Viral matrix protein
Virion
   Coding sequence diversityRibosomal frameshifting
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Magnesium
Metal-binding
Nucleotide-binding
Viral nucleoprotein
Zinc
   Molecular functionAspartyl protease
DNA-directed DNA polymerase
Endonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Protease
RNA-directed DNA polymerase
Transferase
   PTMLipoprotein
Myristate
Phosphoprotein
   Technical termComplete proteome
Direct protein sequencing
Multifunctional enzyme
Reference proteome
Gene Ontology (GO)
   Biological_processDNA integration

Inferred from electronic annotation. Source: UniProtKB-KW

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

dUTP metabolic process

Inferred from electronic annotation. Source: InterPro

establishment of integrated proviral latency

Inferred from electronic annotation. Source: UniProtKB-KW

proteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

viral entry into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentviral nucleocapsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-directed DNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: InterPro

RNA-DNA hybrid ribonuclease activity

Inferred from electronic annotation. Source: UniProtKB-EC

RNA-directed DNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

aspartic-type endopeptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

nucleotide binding

Inferred from electronic annotation. Source: UniProtKB-KW

structural constituent of virion

Inferred from electronic annotation. Source: UniProtKB-KW

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by ribosomal frameshifting. [Align] [Select]

Note: Translation results in the formation of the Gag-Pro. Ribosomal frameshifting at the gag-pro/pol genes boundary produces the Gag-Pro-Pol polyprotein.
Isoform Gag-Pro-Pol polyprotein (identifier: P11283-1)

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.
Note: Produced by -1 ribosomal frameshifting between gag-pro and pro-pol.
Isoform Gag-Pro polyprotein (identifier: Q9IZT2-1)

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.
Isoform Gag polyprotein (identifier: P11284-1)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 17551754Gag-Pro-Pol polyprotein
PRO_0000125493
Chain2 – 9998Matrix protein p10
PRO_0000403612
Chain100 – 19596Phosphorylated protein pp21
PRO_0000403613
Chain196 – 22833Protein p3
PRO_0000403614
Chain229 – 25224Protein p8 Potential
PRO_0000403615
Chain253 – 26917Protein n
PRO_0000403616
Chain270 – 496227Capsid protein p27
PRO_0000403617
Chain497 – 745249Nucleocapsid protein-dUTPase Potential
PRO_0000403618
Chain746 – 83388Protease Potential
PRO_0000403619
Chain834 – 1437604Reverse transcriptase/ribonuclease H Potential
PRO_0000403620
Chain1438 – 1755318Integrase Potential
PRO_0000403621

Regions

Domain766 – 84176Peptidase A2
Domain905 – 1093189Reverse transcriptase
Domain1307 – 1435129RNase H
Domain1490 – 1647158Integrase catalytic
Zinc finger525 – 54218CCHC-type 1
Zinc finger552 – 56918CCHC-type 2
Zinc finger1436 – 147742Integrase-type
DNA binding1653 – 170250Integrase-type By similarity
Compositional bias278 – 2814Poly-Asp
Compositional bias716 – 7194Poly-Leu

Sites

Active site7711Protease; shared with dimeric partner By similarity
Metal binding9701Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding10451Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding10461Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding13161Magnesium; catalytic; for RNase H activity By similarity
Metal binding13461Magnesium; catalytic; for RNase H activity By similarity
Metal binding13661Magnesium; catalytic; for RNase H activity By similarity
Metal binding14291Magnesium; catalytic; for RNase H activity By similarity
Metal binding15011Magnesium; catalytic; for integrase activity By similarity
Metal binding15581Magnesium; catalytic; for integrase activity By similarity
Site99 – 1002Cleavage; by viral protease By similarity
Site195 – 1962Cleavage; by viral protease By similarity
Site228 – 2292Cleavage; by viral protease By similarity
Site252 – 2532Cleavage; by viral protease By similarity
Site269 – 2702Cleavage; by viral protease By similarity
Site496 – 4972Cleavage; by viral protease By similarity
Site745 – 7462Cleavage; by viral protease By similarity
Site833 – 8342Cleavage; by viral protease By similarity
Site1437 – 14382Cleavage; by viral protease By similarity

Amino acid modifications

Lipidation21N-myristoyl glycine; by host By similarity

Natural variations

Natural variant5231E → K.

Experimental info

Sequence conflict857 – 8604SQDL → FTGF in AAA66625. Ref.2
Sequence conflict8671S → T in AAA66625. Ref.2
Sequence conflict9521P → L in AAA66625. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform Gag-Pro-Pol polyprotein [UniParc].

Last modified January 11, 2011. Version 2.
Checksum: 0E99A2ADD96823A4

FASTA1,755197,329
        10         20         30         40         50         60 
MGVSGSKGQK LFVSVLQRLL SERGLHVKES SAIEFYQFLI KVSPWFPEEG GLNLQDWKRV 

        70         80         90        100        110        120 
GREMKKYAAE HGTDSIPKQA YPIWLQLREI LTEQSDLVLL SAEAKSVTEE ELEEGLTGLL 

       130        140        150        160        170        180 
SASSQEKTYG TRGTAYAEID TEVDKLSEHI YDEPYEEKEK ADKNEEKDHV RKVKKIVQRK 

       190        200        210        220        230        240 
ENSEHKRKEK DQKAFLATDW NNDDLSPEDW DDLEEQAAHY HDDDELILPV KRKVDKKKPL 

       250        260        270        280        290        300 
ALRRKPLPPV GFAGAMAEAR EKGDLTFTFP VVFMGESDDD DTPVWEPLPL KTLKELQSAV 

       310        320        330        340        350        360 
RTMGPSAPYT LQVVDMVASQ WLTPSDWHQT ARATLSPGDY VLWRTEYEEK SKETVQKTAG 

       370        380        390        400        410        420 
KRKGKVSLDM LLGTGQFLSP SSQIKLSKDV LKDVTTNAVL AWRAIPPPGV KKTVLAGLKQ 

       430        440        450        460        470        480 
GNEESYETFI SRLEEAVYRM MPRGEGSDIL IKQLAWENAN SLCQDLIRPM RKTGTMQDYI 

       490        500        510        520        530        540 
RACLDASPAV VQGMAYAAAM RGQKYSTFVK QTYGGGKGGQ GSEGPVCFSC GKTGHIKRDC 

       550        560        570        580        590        600 
KEEKGSKRAP PGLCPRCKKG YHWKSECKSK FDKDGNPLPP LETNAENSKN LVKGQSPSPT 

       610        620        630        640        650        660 
QKGDKGKDSG LNPEAPPFTI HDLPRGTPGS AGLDLSSQKD LILSLEDGVS LVPTLVKGTL 

       670        680        690        700        710        720 
PEGTTGLIIG RSSNYKKGLE VLPGVIDSDF QGEIKVMVKA AKNAVIIHKG ERIAQLLLLP 

       730        740        750        760        770        780 
YLKLPNPIIK EERGSEGFGS TSHVHWVQEI SDSRPMLHIS LNGRRFLGLL DTGADKTCIA 

       790        800        810        820        830        840 
GRDWPANWPI HQTESSLQGL GMACGVARSS QPLRWQHEDK SGIIHPFVIP TLPFTLWGRD 

       850        860        870        880        890        900 
IMKEIKVRLM TDSPDDSQDL MIGAIESNLF ADQISWKSDQ PVWLNQWPLK QEKLQALQQL 

       910        920        930        940        950        960 
VTEQLQLGHL EESNSPWNTP VFVIKKKSGK WRLLQDLRAV NATMHDMGAL QPGLPSPVAV 

       970        980        990       1000       1010       1020 
PKGWEIIIID LQDCFFNIKL HPEDCKRFAF SVPSPNFKRP YQRFQWKVLP QGMKNSPTLC 

      1030       1040       1050       1060       1070       1080 
QKFVDKAILT VRDKYQDSYI VHYMDDILLA HPSRSIVDEI LTSMIQALNK HGLVVSTEKI 

      1090       1100       1110       1120       1130       1140 
QKYDNLKYLG THIQGDAVSY QKLQIRTDKL RTLNDFQKLL GNINWIRPFL KLTTGELKPL 

      1150       1160       1170       1180       1190       1200 
FEILNGDSNP ISIRKLTPEA CKALQLVNER LSIARVKRLD LSRPWSLCIL KTEYTPTACL 

      1210       1220       1230       1240       1250       1260 
WQNGVLEWIH LPHISPKVIT PYDIFCTQLI IKGRHRSKEL FSKDPDYIVV PYTKVQFDLL 

      1270       1280       1290       1300       1310       1320 
LQEKEDWPIS LLGFLGEVHF HLPKDPLLTF TLQTAIIFPH MTSTTPLEKG IVIFTDGSAN 

      1330       1340       1350       1360       1370       1380 
GRSVTYIQGR EPIIKENTQN TAQQAEIVAV ITAFEEVSQS FNLYTDSKYV TGLFPEIETA 

      1390       1400       1410       1420       1430       1440 
TLSPRTKIYT ELRHLQRLIH KRQEKFYIGH IRGHTGLPGP LAQGNAYADS LTRILTALES 

      1450       1460       1470       1480       1490       1500 
AQESHALHHQ NAAALRFQFH ITREQAREIV KLCPNCPDWG HAPQLGVNPR GLKPRVLWQM 

      1510       1520       1530       1540       1550       1560 
DVTHVSEFGK LKYVHVTVDT YSHFTFATAR TGEATKDVLQ HLAQSFAYMG FPQKIKTDNA 

      1570       1580       1590       1600       1610       1620 
PAYVSRSIQE FLARWKISHV TGIPYNPQGQ AIVERTHQNI KAQLNKLQKA GKYYTPHHLL 

      1630       1640       1650       1660       1670       1680 
AHALFVLNHV NMDNQGHTAA ERHWGPISAD PKPMVMWKDL LAGSWKGPDV LITAGRGYAC 

      1690       1700       1710       1720       1730       1740 
VFPQDAETPI WVPDRFIRPF TERKEATPTP GTAEKTPPRD EKDQQKSPED ESSPHQREDG 

      1750 
LATSAGVNLR SGGGS 

« Hide

Isoform Gag-Pro polyprotein [UniParc].

See Q9IZT2.

Isoform Gag polyprotein [UniParc].

See P11284.

References

[1]"Genetics of mouse mammary tumor virus-induced mammary tumors: linkage of tumor induction to the gag gene."
Hook L.M., Agafonova Y., Ross S.R., Turner S.J., Golovkina T.V.
J. Virol. 74:8876-8883(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Two efficient ribosomal frameshifting events are required for synthesis of mouse mammary tumor virus gag-related polyproteins."
Jacks T., Townsley K., Varmus H.E., Majors J.
Proc. Natl. Acad. Sci. U.S.A. 84:4298-4302(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 359-591 AND 857-970, RIBOSOMAL FRAMESHIFT.
[3]"Analysis of gag proteins from mouse mammary tumor virus."
Hizi A., Henderson L.E., Copeland T.D., Sowder R.C., Krutzsch H.C., Oroszlan S.
J. Virol. 63:2543-2549(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-58; 65-116; 194-218; 227-241; 251-252; 270-276 AND 362-591, PROTEOLYTIC PROCESSING OF POLYPROTEIN, MYRISTOYLATION AT GLY-2.
[4]"Purification and characterization of the mouse mammary tumor virus protease expressed in Escherichia coli."
Menendez-Arias L., Young M., Oroszlan S.
J. Biol. Chem. 267:24134-24139(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[5]"The protein p30, encoded at the gag-pro junction of mouse mammary tumor virus, is a dUTPase fused with a nucleocapsid protein."
Bergman A.C., Bjornberg O., Nord J., Nyman P.O., Rosengren A.M.
Virology 204:420-424(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: RIBOSOMAL FRAMESHIFT, SUBUNIT, CHARACTERIZATION OF NC-DUTPASE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF228552 Genomic DNA. Translation: AAF31474.1.
M16766 Genomic RNA. Translation: AAA66623.1.
M16766 Genomic RNA. Translation: AAA66625.1.
PIRB29029.

3D structure databases

ProteinModelPortalP11283.
SMRP11283. Positions 550-580, 619-724.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.10.10.200. 1 hit.
1.10.1200.30. 1 hit.
1.10.375.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProIPR001969. Aspartic_peptidase_AS.
IPR003322. B_retro_matrix_N.
IPR008180. dUTP_pyroPase.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamPF00692. 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.
[Graphical view]
ProDomPD004265. B_retro_matrix_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 2 hits.
PROSITEPS50175. 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.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOL_MMTVC
AccessionPrimary (citable) accession number: P11283
Secondary accession number(s): Q9IZT3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: January 11, 2011
Last modified: April 16, 2014
This is version 73 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries