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P0CX76

- YM12A_YEAST

UniProt

P0CX76 - YM12A_YEAST

Protein

Transposon Ty1-ML2 Gag polyprotein

Gene

TY1A-ML2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 25 (01 Oct 2014)
      Sequence version 1 (28 Jun 2011)
      Previous versions | rss
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    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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei401 – 4022Cleavage; by Ty1 proteaseBy similarity

    GO - Molecular functioni

    1. RNA binding Source: SGD

    GO - Biological processi

    1. transposition, RNA-mediated Source: SGD

    Keywords - Ligandi

    RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Transposon Ty1-ML2 Gag polyprotein
    Alternative name(s):
    Gag-p49
    Transposon Ty1 protein A
    Short name:
    TY1A
    Short name:
    TYA
    p58
    Cleaved into the following 2 chains:
    Capsid protein
    Short name:
    CA
    Alternative name(s):
    Gag-p45
    p54
    Gene namesi
    Name:TY1A-ML2
    Synonyms:YMLWTy1-2 GAG
    Ordered Locus Names:YML040W
    ORF Names:YM8054.03
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIII

    Organism-specific databases

    CYGDiYML040w.
    SGDiS000004504. YML040W.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 440440Transposon Ty1-ML2 Gag polyproteinPRO_0000409803Add
    BLAST
    Chaini1 – 401401Capsid proteinBy similarityPRO_0000409804Add
    BLAST
    Peptidei402 – 44039Gag-p4By similarityPRO_0000409805Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei416 – 4161PhosphoserineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Expressioni

    Inductioni

    Ty1-ML2 is a highly expressed element. Induced under amino acid starvation conditions by GCN4.1 Publication

    Interactioni

    Subunit structurei

    Homotrimer.By similarity

    Protein-protein interaction databases

    BioGridi31496. 4 interactions.
    33779. 5 interactions.
    35130. 5 interactions.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni299 – 401103RNA-bindingBy 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

    Phylogenomic databases

    GeneTreeiENSGT00710000106943.
    OrthoDBiEOG7TJ3S3.

    Family and domain databases

    InterProiIPR015820. Retrotransposon_Ty1A_N.
    [Graphical view]
    PfamiPF01021. TYA. 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-ML2 Gag polyprotein (identifier: P0CX76-1) [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

    MESQQLSQHS HISHGSACAS VTSKEVHTNQ DPLDVSASKT EECEKASTKA    50
    NSQQTTTPAS SAVPENPHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG 100
    WSFYGHPSMI PYTPYQMSPM YFPPGPQSQF PQYPSSVGTP LSTPSPESGN 150
    TFTDSSSADS DMTSTKKYVR PPPMLTSPND FPNWVKTYIK FLQNSNLGGI 200
    IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI LSVDYTDIMK 250
    ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN 300
    GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ 350
    QGSRNSKPNY RRNLSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA 400
    HNVSTSNNSP STDNDSISKS TTEPIQLNNK HDLHLRPGTY 440

    Note: Produced by conventional translation.

    Length:440
    Mass (Da):48,993
    Last modified:June 28, 2011 - v1
    Checksum:iACC50DD2AC8F4781
    GO
    Isoform Transposon Ty1-ML2 Gag-Pol polyprotein (identifier: Q03434-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry Q03434.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YML040W ORF.

    Length:1,755
    Mass (Da):198,572
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z48430 Genomic DNA. Translation: CAA88329.1.
    BK006946 Genomic DNA. Translation: DAA09860.1.
    PIRiS57044.
    RefSeqiNP_012561.3. NM_001181684.3. [P0CX76-1]
    NP_013673.1. NM_001182398.1. [P0CX76-1]
    NP_058172.1. NM_001184407.1. [P0CX76-1]

    Genome annotation databases

    EnsemblFungiiYJR026W; YJR026W; YJR026W.
    YLR227W-A; YLR227W-A; YLR227W-A.
    YML040W; YML040W; YML040W.
    GeneIDi850926.
    853483.
    854968.
    KEGGisce:YJR026W.
    sce:YLR227W-A.
    sce:YML040W.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z48430 Genomic DNA. Translation: CAA88329.1 .
    BK006946 Genomic DNA. Translation: DAA09860.1 .
    PIRi S57044.
    RefSeqi NP_012561.3. NM_001181684.3. [P0CX76-1 ]
    NP_013673.1. NM_001182398.1. [P0CX76-1 ]
    NP_058172.1. NM_001184407.1. [P0CX76-1 ]

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31496. 4 interactions.
    33779. 5 interactions.
    35130. 5 interactions.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YJR026W ; YJR026W ; YJR026W .
    YLR227W-A ; YLR227W-A ; YLR227W-A .
    YML040W ; YML040W ; YML040W .
    GeneIDi 850926.
    853483.
    854968.
    KEGGi sce:YJR026W.
    sce:YLR227W-A.
    sce:YML040W.

    Organism-specific databases

    CYGDi YML040w.
    SGDi S000004504. YML040W.

    Phylogenomic databases

    GeneTreei ENSGT00710000106943.
    OrthoDBi EOG7TJ3S3.

    Miscellaneous databases

    NextBioi 967358.

    Family and domain databases

    InterProi IPR015820. Retrotransposon_Ty1A_N.
    [Graphical view ]
    Pfami PF01021. TYA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. 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. "Differential effects of chromatin and Gcn4 on the 50-fold range of expression among individual yeast Ty1 retrotransposons."
      Morillon A., Benard L., Springer M., Lesage P.
      Mol. Cell. Biol. 22:2078-2088(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    5. "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.

    Entry informationi

    Entry nameiYM12A_YEAST
    AccessioniPrimary (citable) accession number: P0CX76
    Secondary accession number(s): D6VWK0, P47097, Q66R50
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 28, 2011
    Last sequence update: June 28, 2011
    Last modified: October 1, 2014
    This is version 25 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, Reference proteome, Transposable element

    Documents

    1. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    2. Yeast chromosome XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    External Data

    Dasty 3