ID   YD21A_YEAST             Reviewed;         438 AA.
AC   Q12392; D6VS20; P87338; Q7LIH4;
DT   06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   08-NOV-2023, entry version 123.
DE   RecName: Full=Transposon Ty2-DR1 Gag polyprotein;
DE   AltName: Full=Transposon Ty2 protein A;
DE            Short=TY2A;
DE            Short=TYA;
DE   AltName: Full=Ty917 protein A;
DE   Contains:
DE     RecName: Full=Capsid protein;
DE              Short=CA;
DE   Contains:
DE     RecName: Full=Gag-p4;
GN   Name=TY2A-DR1; Synonyms=YDRCTy2-1 GAG; OrderedLocusNames=YDR034C-C;
GN   ORFNames=YD9673.06c;
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=9169867;
RA   Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA   Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA   Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA   Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA   Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA   Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA   Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA   Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA   Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA   Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA   Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA   Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA   Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA   Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA   Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA   Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA   Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA   Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA   Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA   Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA   Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA   Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA   Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA   Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA   Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA   Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA   Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA   Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA   Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA   Mewes H.-W., Zollner A., Zaccaria P.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL   Nature 387:75-78(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   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-103.
RX   PubMed=2825192; DOI=10.1073/pnas.84.23.8520;
RA   Liao X.B., Clare J.J., Farabaugh P.J.;
RT   "The upstream activation site of a Ty2 element of yeast is necessary but
RT   not sufficient to promote maximal transcription of the element.";
RL   Proc. Natl. Acad. Sci. U.S.A. 84:8520-8524(1987).
RN   [4]
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   [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 Ty2 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.;
CC       Name=Transposon Ty2-DR1 Gag polyprotein;
CC         IsoId=Q12392-1; Sequence=Displayed;
CC       Name=Transposon Ty2-DR1 Gag-Pol polyprotein;
CC         IsoId=Q12472-1; Sequence=External;
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. Ty2 retrotransposons belong
CC       to the copia elements (pseudoviridae).
CC   -!- MISCELLANEOUS: [Isoform Transposon Ty2-DR1 Gag polyprotein]: Produced
CC       by conventional translation.
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DR   EMBL; Z68196; CAA92373.1; -; Genomic_DNA.
DR   EMBL; Z74330; CAA98858.1; -; Genomic_DNA.
DR   EMBL; Z74331; CAA98860.1; -; Genomic_DNA.
DR   EMBL; M18805; AAA35187.1; -; Genomic_DNA.
DR   EMBL; BK006938; DAA11880.1; -; Genomic_DNA.
DR   PIR; A39980; A39980.
DR   PIR; S61589; S61589.
DR   RefSeq; NP_058139.1; NM_001184378.1. [Q12392-1]
DR   AlphaFoldDB; Q12392; -.
DR   BioGRID; 32085; 16.
DR   MEROPS; A11.003; -.
DR   iPTMnet; Q12392; -.
DR   PaxDb; 4932-YDR034C-C; -.
DR   PeptideAtlas; Q12392; -.
DR   GeneID; 851600; -.
DR   KEGG; sce:YDR034C-C; -.
DR   AGR; SGD:S000007344; -.
DR   SGD; S000007344; YDR034C-C.
DR   VEuPathDB; FungiDB:YDR034C-C; -.
DR   eggNOG; KOG0017; Eukaryota.
DR   HOGENOM; CLU_045291_1_0_1; -.
DR   InParanoid; Q12392; -.
DR   OrthoDB; 2040861at2759; -.
DR   Proteomes; UP000002311; Chromosome IV.
DR   RNAct; Q12392; 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   3: Inferred from homology;
KW   Cytoplasm; Reference proteome; Ribosomal frameshifting; RNA-binding;
KW   Transposable element.
FT   CHAIN           1..438
FT                   /note="Transposon Ty2-DR1 Gag polyprotein"
FT                   /id="PRO_0000279289"
FT   CHAIN           1..397
FT                   /note="Capsid protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279290"
FT   PEPTIDE         398..438
FT                   /note="Gag-p4"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279291"
FT   REGION          1..88
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          295..397
FT                   /note="RNA-binding"
FT                   /evidence="ECO:0000250"
FT   REGION          360..403
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          418..438
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..67
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   SITE            397..398
FT                   /note="Cleavage; by Ty2 protease"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   438 AA;  49689 MW;  1D273B0A0B34C3D1 CRC64;
     MESQQLSQNS PNLHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV NSQQETTPGT
     SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN WAHYQQPSMM TCSHYQTSPA
     YYQPDPHYPL PQYIPPLSTS SPDPIDLKNQ HSEIPQAKTK VGNNVLPPHT LTSEENFSTW
     VKFYIRFLKN SNLGDIIPND QGEIKRQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN
     YADILTVLCK SVSKMQTNNQ ELKDWIALAN LEYDGSTSAD TFEITVSTII QRLKENNINV
     SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN LNKPSQYKQH
     SEYKNVSRTS PNTTNTKVTT RNYQRTNSSK PRAAKAHNIA TSSKFSRVNN DHINESTVSS
     QYLSDDNELS LRPATERI
//