Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P0C2J0

- YP13B_YEAST

UniProt

P0C2J0 - YP13B_YEAST

Protein

Transposon Ty1-PR2 Gag-Pol polyprotein

Gene

TY1B-PR2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 64 (01 Oct 2014)
      Sequence version 1 (06 Mar 2007)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome. The particles are assembled from trimer-clustered units and there are holes in the capsid shells that allow for the diffusion of macromolecules. CA has also nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty1 RNA and initiation of reverse transcription By similarity.By similarity
    The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.By similarity
    Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The 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 during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends By similarity.By similarity
    Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome By similarity.By similarity

    Catalytic activityi

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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei401 – 4022Cleavage; by Ty1 proteaseBy similarity
    Active sitei461 – 4611For protease activity; shared with dimeric partnerPROSITE-ProRule annotation
    Sitei582 – 5832Cleavage; by Ty1 proteaseBy similarity
    Metal bindingi671 – 6711Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi736 – 7361Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Sitei1218 – 12192Cleavage; by Ty1 proteaseBy similarity
    Metal bindingi1347 – 13471Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1428 – 14281Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1429 – 14291Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1611 – 16111Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1653 – 16531Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1686 – 16861Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: UniProtKB-KW
    2. ATP binding Source: UniProtKB-KW
    3. DNA binding Source: UniProtKB-KW
    4. DNA-directed DNA polymerase activity Source: SGD
    5. metal ion binding Source: UniProtKB-KW
    6. peptidase activity Source: SGD
    7. ribonuclease activity Source: SGD
    8. RNA binding Source: SGD
    9. RNA-directed DNA polymerase activity Source: SGD
    10. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

    GO - Biological processi

    1. DNA-dependent DNA replication Source: GOC
    2. DNA integration Source: UniProtKB-KW
    3. DNA recombination Source: UniProtKB-KW
    4. RNA-dependent DNA replication Source: GOC
    5. RNA phosphodiester bond hydrolysis Source: GOC
    6. transposition, RNA-mediated Source: SGD
    7. viral release from host cell Source: UniProtKB-KW

    Keywords - Molecular functioni

    Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

    Keywords - Biological processi

    DNA integration, DNA recombination, Transposition, Virion maturation, Virus exit from host cell

    Keywords - Ligandi

    ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Transposon Ty1-PR2 Gag-Pol polyprotein
    Alternative name(s):
    Gag-Pol-p199
    TY1A-TY1B
    Transposon Ty1 TYA-TYB polyprotein
    p190
    Cleaved into the following 4 chains:
    Capsid protein
    Short name:
    CA
    Alternative name(s):
    Gag-p45
    p54
    Ty1 protease (EC:3.4.23.-)
    Short name:
    PR
    Alternative name(s):
    Pol-p20
    p23
    Integrase
    Short name:
    IN
    Alternative name(s):
    Pol-p71
    p84
    p90
    Reverse transcriptase/ribonuclease H (EC:2.7.7.49, EC:2.7.7.7, EC:3.1.26.4)
    Short name:
    RT
    Short name:
    RT-RH
    Alternative name(s):
    Pol-p63
    p60
    Gene namesi
    Name:TY1B-PR2
    Synonyms:YPRWTy1-3 POL
    Ordered Locus Names:YPR158W-B
    ORF Names:P9584.3c
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XVI

    Organism-specific databases

    SGDiS000007364. YPR158W-B.

    Subcellular locationi

    Cytoplasm. Nucleus By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleus Source: SGD
    3. retrotransposon nucleocapsid Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 17561756Transposon Ty1-PR2 Gag-Pol polyproteinPRO_0000279179Add
    BLAST
    Chaini1 – 401401Capsid proteinBy similarityPRO_0000279180Add
    BLAST
    Chaini402 – 582181Ty1 proteaseBy similarityPRO_0000279181Add
    BLAST
    Chaini583 – 1218636IntegraseBy similarityPRO_0000279182Add
    BLAST
    Chaini1219 – 1756538Reverse transcriptase/ribonuclease HBy similarityPRO_0000279183Add
    BLAST

    Post-translational modificationi

    Initially, virus-like particles (VLPs) are composed of the structural unprocessed proteins Gag and Gag-Pol, and contain also the host initiator methionine tRNA (tRNA(i)-Met) which serves as a primer for minus-strand DNA synthesis, and a dimer of genomic Ty RNA. Processing of the polyproteins occurs within the particle and proceeds by an ordered pathway, called maturation. First, the protease (PR) is released by autocatalytic cleavage of the Gag-Pol polyprotein yielding capsid protein p45 and a Pol-p154 precursor protein. This cleavage is a prerequisite for subsequent processing of Pol-p154 at the remaining sites to release the mature structural and catalytic proteins. Maturation takes place prior to the RT reaction and is required to produce transposition-competent VLPs By similarity.By similarity

    Expressioni

    Gene expression databases

    GenevestigatoriP0C2J0.

    Interactioni

    Subunit structurei

    The capsid protein forms a homotrimer, from which the VLPs are assembled. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues By similarity.By similarity

    Protein-protein interaction databases

    BioGridi36327. 3 interactions.
    IntActiP0C2J0. 2 interactions.
    MINTiMINT-7980680.
    STRINGi4932.YPR158W-B.

    Structurei

    3D structure databases

    ProteinModelPortaliP0C2J0.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini660 – 836177Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST
    Domaini1339 – 1477139Reverse transcriptase Ty1/copia-typeAdd
    BLAST
    Domaini1611 – 1753143RNase H Ty1/copia-typeAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni299 – 401103RNA-bindingBy similarityAdd
    BLAST
    Regioni583 – 64058Integrase-type zinc finger-likeAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1179 – 121335Bipartite nuclear localization signalBy similarityAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi64 – 14683Pro-richAdd
    BLAST

    Domaini

    The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities.By similarity
    Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.By similarity

    Sequence similaritiesi

    Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
    Contains 1 peptidase A11 domain.Curated

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    GeneTreeiENSGT00730000111405.
    HOGENOMiHOG000280731.
    OrthoDBiEOG7TJ3S3.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    InterProiIPR001969. Aspartic_peptidase_AS.
    IPR001584. Integrase_cat-core.
    IPR015820. Retrotransposon_Ty1A_N.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    [Graphical view]
    PfamiPF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    PF01021. TYA. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    PROSITEiPS00141. ASP_PROTEASE. 1 hit.
    PS50994. INTEGRASE. 1 hit.
    [Graphical view]

    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. Align

    Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift. The ratio of Gag:Gag-Pol varies between 20:1 and 5:1 (By similarity).By similarity

    Isoform Transposon Ty1-PR2 Gag-Pol polyprotein (identifier: P0C2J0-1) [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

    MESQQLSNYP HISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA     50
    NSQQTTTPAS SAVPENPHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG 100
    WSFYGHPSMI PYTPYQMSPM YFPPGPQSQF PQYPSSVGTP LSTPSPESGN 150
    TFTDSSSADS DMTSTKKYVR PPPMLTSPND FPNWVKTYIK FLQNSNLGGI 200
    IPTVNGKPVR PITDDELTFL YNTFQIFAPS QFLPTWVKDI LSVDYTDIMK 250
    ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN 300
    GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ 350
    QGSRNSKPNY RRNPSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA 400
    HNVSTSNNSP STDNDSISKS TTEPIQLNNK HDLHLGQKLT ESTVNHTNHS 450
    DDELPGHLLL DSGASRTLIR SAHHIHSASS NPDINVVDAQ KRNIPINAIG 500
    DLQFHFQDNT KTSIKVLHTP NIAYDLLSLN ELAAVDITAC FTKNVLERSD 550
    GTVLAPIVKY GDFYWVSKKY LLPSNISVPT INNVHTSEST RKYPYPFIHR 600
    MLAHANAQTI RYSLKNNTIT YFNESDVDWS SAIDYQCPDC LIGKSTKHRH 650
    IKGSRLKYQN SYEPFQYLHT DIFGPVHNLP KSAPSYFISF TDETTKFRWV 700
    YPLHDRREDS ILDVFTTILA FIKNQFQASV LVIQMDRGSE YTNRTLHKFL 750
    EKKNGITPCY TTTADSRAHG VAERLNRTLL DDCRTQLQCS GLPNHLWFSA 800
    IEFSTIVRNS LASPKSKKSA RQHAGLAGLD ISTLLPFGQP VIVNDHNPNS 850
    KIHPRGIPGY ALHPSRNSYG YIIYLPSLKK TVDTTNYVIL QGKESRLDQF 900
    NYDALTFDED LNRLTASYHS FIASNEIQES NDLNIESDHD FQSDIELHPE 950
    QPRNVLSKAV SPTDSTPPST HTEDSKRVSK TNIRAPREVD PNISESNILP 1000
    SKKRSSTPQI SNIESTGSGG MHKLNVPLLA PMSQSNTHES SHASKSKDFR 1050
    HSDSYSENET NHTNVPISST GGTNNKTVPQ ISDQETEKRI IHRSPSIDAS 1100
    PPENNSSHNI VPIKTPTTVS EQNTEESIIA DLPLPDLPPE SPTEFPDPFK 1150
    ELPPINSHQT NSSLGGIGDS NAYTTINSKK RSLEDNETEI KVSRDTWNTK 1200
    NMRSLEPPRS KKRIHLIAAV KAVKSIKPIR TTLRYDEAIT YNKDIKEKEK 1250
    YIEAYHKEVN QLLKMNTWDT DKYYDRKEID PKRVINSMFI FNRKRDGTHK 1300
    ARFVARGDIQ HPDTYDSGMQ SNTVHHYALM TSLSLALDNN YYITQLDISS 1350
    AYLYADIKEE LYIRPPPHLG MNDKLIRLKK SLYGLKQSGA NWYETIKSYL 1400
    IKQCGMEEVR GWSCVFKNSQ VTICLFVDDM ILFSKDLNAN KKIITTLKKQ 1450
    YDTKIINLGE SDNEIQYDIL GLEIKYQRGK YMKLGMENSL TEKIPKLNVP 1500
    LNPKGRKLSA PGQPGLYIDQ DELEIDEDEY KEKVHEMQKL IGLASYVGYK 1550
    FRFDLLYYIN TLAQHILFPS RQVLDMTYEL IQFMWDTRDK QLIWHKNKPT 1600
    EPDNKLVAIS DASYGNQPYY KSQIGNIYLL NGKVIGGKST KASLTCTSTT 1650
    EAEIHAISES VPLLNNLSHL VQELNKKPIT KGLLTDSKST ISIIISNNEE 1700
    KFRNRFFGTK AMRLRDEVSG NHLHVCYIET KKNIADVMTK PLPIKTFKLL 1750
    TNKWIH 1756

    Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YPR158W-A ORF.

    Length:1,756
    Mass (Da):198,639
    Last modified:March 6, 2007 - v1
    Checksum:iECBC18448B722BF6
    GO
    Isoform Transposon Ty1-PR2 Gag polyprotein (identifier: P0CX60-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry P0CX60.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:440
    Mass (Da):49,098
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U28371 Genomic DNA. No translation available.
    BK006949 Genomic DNA. Translation: DAA11571.1.
    PIRiS69983.
    RefSeqiNP_058193.1. NM_001184398.1. [P0C2J0-1]

    Genome annotation databases

    EnsemblFungiiYPR158W-B; YPR158W-B; YPR158W-B. [P0C2J0-1]
    GeneIDi856283.
    KEGGisce:YPR158W-B.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U28371 Genomic DNA. No translation available.
    BK006949 Genomic DNA. Translation: DAA11571.1 .
    PIRi S69983.
    RefSeqi NP_058193.1. NM_001184398.1. [P0C2J0-1 ]

    3D structure databases

    ProteinModelPortali P0C2J0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36327. 3 interactions.
    IntActi P0C2J0. 2 interactions.
    MINTi MINT-7980680.
    STRINGi 4932.YPR158W-B.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YPR158W-B ; YPR158W-B ; YPR158W-B . [P0C2J0-1 ]
    GeneIDi 856283.
    KEGGi sce:YPR158W-B.

    Organism-specific databases

    SGDi S000007364. YPR158W-B.

    Phylogenomic databases

    GeneTreei ENSGT00730000111405.
    HOGENOMi HOG000280731.
    OrthoDBi EOG7TJ3S3.

    Miscellaneous databases

    NextBioi 981610.

    Gene expression databases

    Genevestigatori P0C2J0.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    InterProi IPR001969. Aspartic_peptidase_AS.
    IPR001584. Integrase_cat-core.
    IPR015820. Retrotransposon_Ty1A_N.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    [Graphical view ]
    Pfami PF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    PF01021. TYA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    PROSITEi PS00141. ASP_PROTEASE. 1 hit.
    PS50994. INTEGRASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
      Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
      , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
      Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence."
      Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.
      Genome Res. 8:464-478(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NOMENCLATURE.
    4. "Happy together: the life and times of Ty retrotransposons and their hosts."
      Lesage P., Todeschini A.L.
      Cytogenet. Genome Res. 110:70-90(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    5. "Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1 element."
      Wilhelm F.-X., Wilhelm M., Gabriel A.
      Cytogenet. Genome Res. 110:269-287(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW, DOMAINS.

    Entry informationi

    Entry nameiYP13B_YEAST
    AccessioniPrimary (citable) accession number: P0C2J0
    Secondary accession number(s): D6W4F5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 6, 2007
    Last sequence update: March 6, 2007
    Last modified: October 1, 2014
    This is version 64 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Retrotransposons are mobile genetic entities that are able to replicate via an RNA intermediate and a reverse transcription step. In contrast to retroviruses, retrotransposons are non-infectious, lack an envelope and remain intracellular. Ty1 retrotransposons belong to the copia elements (pseudoviridae).

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XVI
      Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

    External Data

    Dasty 3