ID   YB11A_YEAST             Reviewed;         440 AA.
AC   Q12266; D6VPZ7;
DT   06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   24-JAN-2024, entry version 129.
DE   RecName: Full=Transposon Ty1-BL 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-BL; Synonyms=YBLWTy1-1 GAG; OrderedLocusNames=YBL005W-A;
GN   ORFNames=YBL004W-B, YBL0324;
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=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA   Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA   Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA   Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA   Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA   Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA   Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA   Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA   Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA   Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA   Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA   Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA   Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA   Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA   Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA   Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA   Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA   Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA   Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA   Mewes H.-W., Kleine K.;
RT   "Complete DNA sequence of yeast chromosome II.";
RL   EMBO J. 13:5795-5809(1994).
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).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [7]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [8]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT   into evolution.";
RL   Science 325:1682-1686(2009).
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-BL Gag polyprotein;
CC         IsoId=Q12266-1; Sequence=Displayed;
CC       Name=Transposon Ty1-BL Gag-Pol polyprotein;
CC         IsoId=Q12490-1; Sequence=External;
CC   -!- INDUCTION: Ty1-BL is a highly 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-BL Gag polyprotein]: Produced by
CC       conventional translation.
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DR   EMBL; Z35765; CAA84819.1; -; Genomic_DNA.
DR   EMBL; Z35766; CAA84823.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07117.1; -; Genomic_DNA.
DR   PIR; S45737; S45737.
DR   RefSeq; NP_009550.1; NM_001180047.1. [Q12266-1]
DR   AlphaFoldDB; Q12266; -.
DR   SMR; Q12266; -.
DR   BioGRID; 32695; 7.
DR   IntAct; Q12266; 2.
DR   iPTMnet; Q12266; -.
DR   PaxDb; 4932-YBL005W-A; -.
DR   PeptideAtlas; Q12266; -.
DR   GeneID; 852279; -.
DR   KEGG; sce:YBL005W-A; -.
DR   AGR; SGD:S000002146; -.
DR   SGD; S000002146; YBL005W-A.
DR   VEuPathDB; FungiDB:YBL005W-A; -.
DR   eggNOG; KOG0017; Eukaryota.
DR   HOGENOM; CLU_045291_1_0_1; -.
DR   InParanoid; Q12266; -.
DR   OrthoDB; 2039326at2759; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; Q12266; 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   1: Evidence at protein level;
KW   Cytoplasm; Reference proteome; Ribosomal frameshifting; RNA-binding;
KW   Transposable element.
FT   CHAIN           1..440
FT                   /note="Transposon Ty1-BL Gag polyprotein"
FT                   /id="PRO_0000278990"
FT   CHAIN           1..401
FT                   /note="Capsid protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000278991"
FT   PEPTIDE         402..440
FT                   /note="Gag-p4"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000278992"
FT   REGION          20..84
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          137..173
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..424
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        20..67
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;  49285 MW;  EBE246012C88C029 CRC64;
     MESQQLSQHS PIFHGSACAS VTSKEVQTTQ DPLDISASKT EECEKVSTQA NSQQPTTPPS
     SAVPENHHHA SPQAAQVPLP QNGPYPQQRM MNTQQANISG WPVYGHPSLM PYPPYQMSPM
     YAPPGAQSQF TQYPQYVGTH LNTPSPESGN SFPDSSSAKS NMTSTNQHVR PPPILTSPND
     FLNWVKIYIK FLQNSNLGDI IPTATRKAVR QMTDDELTFL CHTFQLFAPS QFLPPWVKDI
     LSVDYTDIMK ILSKSINKMQ SDTQEVNDIT TLATLHYNGS TPADAFEAEV TNILDRLNNN
     GIPINNKVAC QFIMRGLSGE YKFLPYARHR CIHMTVADLF SDIHSMYEEQ QESKRNKSTY
     RRSPSDEKKD SRTYTNTTKP KSITRNSQKP NNSQSRTARA HNVSTFNNSP GPDNDLIRGS
     TTEPIQLKNT HDLHLRPGTY
//