ID   YN11A_YEAST             Reviewed;         440 AA.
AC   Q12391; D6W0Q9;
DT   06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   08-NOV-2023, entry version 124.
DE   RecName: Full=Transposon Ty1-NL1 Gag polyprotein;
DE   AltName: Full=Gag-p49;
DE   AltName: Full=Transposon Ty1 protein A;
DE            Short=TY1A;
DE            Short=TYA;
DE   AltName: Full=p58;
DE   Contains:
DE     RecName: Full=Capsid protein;
DE              Short=CA;
DE     AltName: Full=Gag-p45;
DE     AltName: Full=p54;
DE   Contains:
DE     RecName: Full=Gag-p4;
GN   Name=TY1A-NL1; Synonyms=YNLCTy1-1 GAG; OrderedLocusNames=YNL284C-A;
GN   ORFNames=N0569;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169873;
RA   Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA   Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA   Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA   Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA   Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA   Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA   Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA   Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA   Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA   Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA   Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA   Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA   Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA   Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA   Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA   Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA   Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT   evolutionary implications.";
RL   Nature 387:93-98(1997).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [3]
RP   NOMENCLATURE.
RX   PubMed=9582191; DOI=10.1101/gr.8.5.464;
RA   Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.;
RT   "Transposable elements and genome organization: a comprehensive survey of
RT   retrotransposons revealed by the complete Saccharomyces cerevisiae genome
RT   sequence.";
RL   Genome Res. 8:464-478(1998).
RN   [4]
RP   INDUCTION.
RX   PubMed=11884596; DOI=10.1128/mcb.22.7.2078-2088.2002;
RA   Morillon A., Benard L., Springer M., Lesage P.;
RT   "Differential effects of chromatin and Gcn4 on the 50-fold range of
RT   expression among individual yeast Ty1 retrotransposons.";
RL   Mol. Cell. Biol. 22:2078-2088(2002).
RN   [5]
RP   REVIEW.
RX   PubMed=16093660; DOI=10.1159/000084940;
RA   Lesage P., Todeschini A.L.;
RT   "Happy together: the life and times of Ty retrotransposons and their
RT   hosts.";
RL   Cytogenet. Genome Res. 110:70-90(2005).
CC   -!- FUNCTION: Capsid protein (CA) is the structural component of the virus-
CC       like particle (VLP), forming the shell that encapsulates the
CC       retrotransposons dimeric RNA genome. The particles are assembled from
CC       trimer-clustered units and there are holes in the capsid shells that
CC       allow for the diffusion of macromolecules. CA has also nucleocapsid-
CC       like chaperone activity, promoting primer tRNA(i)-Met annealing to the
CC       multipartite primer-binding site (PBS), dimerization of Ty1 RNA and
CC       initiation of reverse transcription (By similarity). {ECO:0000250}.
CC   -!- SUBUNIT: Homotrimer. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Ribosomal frameshifting; Named isoforms=2;
CC         Comment=The Gag-Pol polyprotein is generated by a +1 ribosomal
CC         frameshift. The ratio of Gag:Gag-Pol varies between 20:1 and 5:1 (By
CC         similarity). {ECO:0000250};
CC       Name=Transposon Ty1-NL1 Gag polyprotein;
CC         IsoId=Q12391-1; Sequence=Displayed;
CC       Name=Transposon Ty1-NL1 Gag-Pol polyprotein;
CC         IsoId=Q12112-1; Sequence=External;
CC   -!- INDUCTION: Ty1-NL1 is a weakly expressed element. Induced under amino
CC       acid starvation conditions by GCN4. {ECO:0000269|PubMed:11884596}.
CC   -!- DOMAIN: The C-terminal RNA-binding region of CA is sufficient for all
CC       its nucleocapsid-like chaperone activities. {ECO:0000250}.
CC   -!- MISCELLANEOUS: Retrotransposons are mobile genetic entities that are
CC       able to replicate via an RNA intermediate and a reverse transcription
CC       step. In contrast to retroviruses, retrotransposons are non-infectious,
CC       lack an envelope and remain intracellular. Ty1 retrotransposons belong
CC       to the copia elements (pseudoviridae).
CC   -!- MISCELLANEOUS: [Isoform Transposon Ty1-NL1 Gag polyprotein]: Produced
CC       by conventional translation.
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DR   EMBL; Z71560; CAA96197.1; -; Genomic_DNA.
DR   EMBL; Z71561; CAA96202.1; -; Genomic_DNA.
DR   EMBL; BK006947; DAA10275.1; -; Genomic_DNA.
DR   PIR; S69970; S69970.
DR   RefSeq; NP_058179.1; NM_001184414.1. [Q12391-1]
DR   AlphaFoldDB; Q12391; -.
DR   SMR; Q12391; -.
DR   BioGRID; 35554; 19.
DR   IntAct; Q12391; 1.
DR   iPTMnet; Q12391; -.
DR   MaxQB; Q12391; -.
DR   PaxDb; 4932-YNL284C-A; -.
DR   PeptideAtlas; Q12391; -.
DR   GeneID; 855434; -.
DR   KEGG; sce:YNL284C-A; -.
DR   AGR; SGD:S000007386; -.
DR   SGD; S000007386; YNL284C-A.
DR   VEuPathDB; FungiDB:YNL284C-A; -.
DR   eggNOG; KOG0017; Eukaryota.
DR   HOGENOM; CLU_045291_1_0_1; -.
DR   InParanoid; Q12391; -.
DR   OrthoDB; 2039326at2759; -.
DR   Proteomes; UP000002311; Chromosome XIV.
DR   RNAct; Q12391; Protein.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0000943; C:retrotransposon nucleocapsid; ISS:SGD.
DR   GO; GO:0003723; F:RNA binding; ISS:SGD.
DR   GO; GO:0032197; P:retrotransposition; ISS:SGD.
DR   InterPro; IPR015820; TYA.
DR   Pfam; PF01021; TYA; 1.
PE   2: Evidence at transcript level;
KW   Cytoplasm; Reference proteome; Ribosomal frameshifting; RNA-binding;
KW   Transposable element.
FT   CHAIN           1..440
FT                   /note="Transposon Ty1-NL1 Gag polyprotein"
FT                   /id="PRO_0000279142"
FT   CHAIN           1..401
FT                   /note="Capsid protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279143"
FT   PEPTIDE         402..440
FT                   /note="Gag-p4"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279144"
FT   REGION          1..86
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          131..171
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          299..401
FT                   /note="RNA-binding"
FT                   /evidence="ECO:0000250"
FT   REGION          350..425
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        131..164
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        350..375
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        376..424
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   SITE            401..402
FT                   /note="Cleavage; by Ty1 protease"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   440 AA;  49309 MW;  173DE7FDF7C2102A CRC64;
     MESQQLSQHS PISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA NSQQTTTPAS
     SAVPENPHHA SPQTAQSHSP QNGPYQQQCM MTQNQANPSG WSFYGRPSMI PYTPYQMSPM
     YFPPGPHSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND
     FLNWVKTYIK FLQNSNLGDI IPTATRKAVR QMTDDELTFL CHTFQLFAPS QFLPTWVKDI
     LSADYTDIMK ILSKSINKMQ SDTQEVNDIT TLATLHYNGS TPADAFEAEV TNILDRLNNN
     GIPINNKVAC QFIMRGLSGE YKFLRYARHR YIHMTVADLF SDIHSMYEEQ QESKRNKSTY
     RRNPSDEKKD SRTYTNTTKP KSITRNSQKP NNSQSRTARA HNVSTSNNSS GPDNDLIRGS
     TTEPIQLKNK HDLHLRPGTY
//