ID   YJ41B_YEAST             Reviewed;        1803 AA.
AC   P47024; D6VW70; P87192;
DT   01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT   02-NOV-2010, sequence version 3.
DT   24-JAN-2024, entry version 142.
DE   RecName: Full=Transposon Ty4-J Gag-Pol polyprotein;
DE   AltName: Full=TY4A-TY4B;
DE   AltName: Full=Transposon Ty4 TYA-TYB polyprotein;
DE   Includes:
DE     RecName: Full=Capsid protein;
DE              Short=CA;
DE   Includes:
DE     RecName: Full=Ty4 protease;
DE              Short=PR;
DE              EC=3.4.23.-;
DE   Includes:
DE     RecName: Full=Integrase;
DE              Short=IN;
DE   Includes:
DE     RecName: Full=Reverse transcriptase/ribonuclease H;
DE              Short=RT;
DE              Short=RT-RH;
DE              EC=2.7.7.49;
DE              EC=2.7.7.7;
DE              EC=3.1.26.4;
GN   Name=TY4B-J; Synonyms=YJLWTy4-1 POL; OrderedLocusNames=YJL113W;
GN   ORFNames=J0780;
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 [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=1328182; DOI=10.1016/s0021-9258(19)88624-6;
RA   Janetzky B., Lehle L.;
RT   "Ty4, a new retrotransposon from Saccharomyces cerevisiae, flanked by tau-
RT   elements.";
RL   J. Biol. Chem. 267:19798-19805(1992).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 96604 / S288c / FY1679;
RX   PubMed=8948101;
RX   DOI=10.1002/(sici)1097-0061(199611)12:14<1471::aid-yea30>3.0.co;2-4;
RA   Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C.;
RT   "Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19
RT   open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14,
RT   RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta
RT   elements and a Ty4 transposon.";
RL   Yeast 12:1471-1474(1996).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA   Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA   Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA   Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA   Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA   Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA   Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA   Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA   Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA   Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA   To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA   von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT   "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL   EMBO J. 15:2031-2049(1996).
RN   [4]
RP   GENOME REANNOTATION, AND SEQUENCE REVISION TO 226 AND 240.
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   [5]
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   [6]
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. {ECO:0000250}.
CC   -!- FUNCTION: The aspartyl protease (PR) mediates the proteolytic cleavages
CC       of the Gag and Gag-Pol polyproteins after assembly of the VLP.
CC       {ECO:0000250}.
CC   -!- FUNCTION: Reverse transcriptase/ribonuclease H (RT) is a
CC       multifunctional enzyme that catalyzes the conversion of the retro-
CC       elements RNA genome into dsDNA within the VLP. The enzyme displays a
CC       DNA polymerase activity that can copy either DNA or RNA templates, and
CC       a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-
CC       DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA
CC       primers. The conversion leads to a linear dsDNA copy of the
CC       retrotransposon that includes long terminal repeats (LTRs) at both ends
CC       (By similarity). {ECO:0000250}.
CC   -!- FUNCTION: Integrase (IN) targets the VLP to the nucleus, where a
CC       subparticle preintegration complex (PIC) containing at least integrase
CC       and the newly synthesized dsDNA copy of the retrotransposon must
CC       transit the nuclear membrane. Once in the nucleus, integrase performs
CC       the integration of the dsDNA into the host genome (By similarity).
CC       {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.49;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.7;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC   -!- SUBUNIT: The protease is a homodimer, whose active site consists of two
CC       apposed aspartic acid residues. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus {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 Ty4-J Gag-Pol polyprotein;
CC         IsoId=P47024-1; Sequence=Displayed;
CC       Name=Transposon Ty4-J Gag polyprotein;
CC         IsoId=P47023-1; Sequence=External;
CC   -!- DOMAIN: Integrase core domain contains the D-x(n)-D-x(35)-E motif,
CC       named for the phylogenetically conserved glutamic acid and aspartic
CC       acid residues and the invariant 35 amino acid spacing between the
CC       second and third acidic residues. Each acidic residue of the D,D(35)E
CC       motif is independently essential for the 3'-processing and strand
CC       transfer activities of purified integrase protein (By similarity).
CC       {ECO:0000250}.
CC   -!- PTM: Proteolytically processed into capsid protein (CA), Ty4 protease
CC       (PR), integrase (IN) and reverse transcriptase/ribonuclease H (RT)
CC       proteins (Probable). Initially, virus-like particles (VLPs) are
CC       composed of the structural unprocessed proteins Gag and Gag-Pol, and
CC       also contain the host initiator methionine tRNA (tRNA(i)-Met) which
CC       serves as a primer for minus-strand DNA synthesis, and a dimer of
CC       genomic Ty RNA. Processing of the polyproteins occurs within the
CC       particle and proceeds by an ordered pathway, called maturation. First,
CC       the protease (PR) is released by autocatalytic cleavage of the Gag-Pol
CC       polyprotein, and this cleavage is a prerequisite for subsequent
CC       processing at the remaining sites to release the mature structural and
CC       catalytic proteins. Maturation takes place prior to the RT reaction and
CC       is required to produce transposition-competent VLPs (By similarity).
CC       {ECO:0000250, ECO:0000305}.
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. Ty4 retrotransposons belong
CC       to the copia elements (pseudoviridae).
CC   -!- MISCELLANEOUS: [Isoform Transposon Ty4-J Gag-Pol polyprotein]: Produced
CC       by +1 ribosomal frameshifting between codon Leu-363 and Gly-364 of the
CC       YJL114W ORF.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAA89409.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=DAA08686.2; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; X67284; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; Z49389; CAA89409.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; BK006943; DAA08686.2; ALT_FRAME; Genomic_DNA.
DR   PIR; S31262; S31262.
DR   PIR; S56894; S56894.
DR   RefSeq; NP_012421.2; NM_001181546.3.
DR   AlphaFoldDB; P47024; -.
DR   BioGRID; 33642; 20.
DR   IntAct; P47024; 6.
DR   MINT; P47024; -.
DR   PeptideAtlas; P47024; -.
DR   GeneID; 853330; -.
DR   KEGG; sce:YJL113W; -.
DR   AGR; SGD:S000003649; -.
DR   SGD; S000003649; YJL113W.
DR   InParanoid; P47024; -.
DR   OrthoDB; 2039886at2759; -.
DR   BioGRID-ORCS; 853330; 0 hits in 10 CRISPR screens.
DR   Proteomes; UP000002311; Chromosome X.
DR   RNAct; P47024; Protein.
DR   GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0000943; C:retrotransposon nucleocapsid; ISS:SGD.
DR   GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; ISS:SGD.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008233; F:peptidase activity; ISS:SGD.
DR   GO; GO:0003723; F:RNA binding; ISS:SGD.
DR   GO; GO:0004540; F:RNA nuclease activity; ISS:SGD.
DR   GO; GO:0003964; F:RNA-directed DNA polymerase activity; ISS:SGD.
DR   GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
DR   GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0032197; P:retrotransposition; ISS:SGD.
DR   CDD; cd09272; RNase_HI_RT_Ty1; 1.
DR   Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 2.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR001584; Integrase_cat-core.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR036397; RNaseH_sf.
DR   InterPro; IPR013103; RVT_2.
DR   PANTHER; PTHR42648; TRANSPOSASE, PUTATIVE-RELATED; 1.
DR   PANTHER; PTHR42648:SF11; TRANSPOSON TY4-P GAG-POL POLYPROTEIN; 1.
DR   Pfam; PF00665; rve; 1.
DR   Pfam; PF07727; RVT_2; 1.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   SUPFAM; SSF53098; Ribonuclease H-like; 1.
DR   PROSITE; PS50994; INTEGRASE; 1.
PE   3: Inferred from homology;
KW   Aspartyl protease; ATP-binding; Coiled coil; Cytoplasm; DNA integration;
KW   DNA recombination; DNA-binding; DNA-directed DNA polymerase; Endonuclease;
KW   Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme; Nuclease;
KW   Nucleotide-binding; Nucleotidyltransferase; Nucleus; Protease;
KW   Reference proteome; Ribosomal frameshifting; RNA-binding;
KW   RNA-directed DNA polymerase; Transferase; Transposable element;
KW   Transposition; Viral release from host cell; Virion maturation; Zinc;
KW   Zinc-finger.
FT   CHAIN           1..1803
FT                   /note="Transposon Ty4-J Gag-Pol polyprotein"
FT                   /id="PRO_0000203502"
FT   DOMAIN          620..787
FT                   /note="Integrase catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   DOMAIN          1376..1511
FT                   /note="Reverse transcriptase Ty1/copia-type"
FT   DOMAIN          1645..1791
FT                   /note="RNase H Ty1/copia-type"
FT   REGION          382..502
FT                   /note="Ty4 protease"
FT   REGION          540..600
FT                   /note="Integrase-type zinc finger-like"
FT   REGION          1224..1250
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          39..115
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        1233..1250
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        415
FT                   /note="For protease activity; shared with dimeric partner"
FT                   /evidence="ECO:0000250"
FT   BINDING         631
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         696
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         1384
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for reverse transcriptase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         1463
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for reverse transcriptase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         1464
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for reverse transcriptase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         1645
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         1687
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   BINDING         1721
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   CONFLICT        452
FT                   /note="V -> L (in Ref. 1; X67284)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        684
FT                   /note="T -> A (in Ref. 1; X67284)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        920
FT                   /note="A -> S (in Ref. 1; X67284)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1020
FT                   /note="S -> R (in Ref. 1; X67284)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1803
FT                   /note="Y -> YLINEVLNTQISVEVQ (in Ref. 1; X67284)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1803 AA;  207710 MW;  A58D1D4E96F7C9C9 CRC64;
     MATPVRGETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVRQ YQRNLNRFKT
     ILNGLKAEEE KLSEADDIQM LAEKLLKLGE TIDKVENRIV DLVEKIQLLE TNENNNILHE
     HIDATGTYYL FDTLTSTNKR FYPKDCVFDY RTNNVENIPI LLNNFKKFIK KYQFDDVFEN
     DIIEIDPREN EILCKIIKEG LGESLDIMNT NTTDIFRIID GLKKQNIEVC MVEMSELEPG
     EKVLVDTTCR NSALLMNKLQ KLVLMEKWIF SKCCQDCPNL KDYLQEAIMG TLHESLRNSV
     KQRLYNIPHD VGIDHEEFLI NTVIETVIDL SPIADDQIEN SCMYCKSVFH CSINCKKKPN
     RELGLTRPIS QKPIIYKVHR DNNHLSPVQN EQKSWNKTQK RSNKVYNSKK LVIIDTGSGV
     NITNDKTLLH NYEDSNRSTR FFGIGKNSSV SVKGYGYIKI KNGHNNTDNK CLLTYYVPEE
     ESTIISCYDL AKKTKMVLSR KYTRLGNKII KIKTKIVNGV IHVKMNELIE RPSDDSKINA
     IKPTSSPGFK LNKRSITLED AHKRMGHTGI QQIENSIKHN HYEESLDLIK EPNEFWCQTC
     KISKATKRNH YTGSMNNHST DHEPGSSWCM DIFGPVSSSN ADTKRYMLIM VDNNTRYCMT
     STHFNKNAET ILAQVRKNIQ YVETQFDRKV REINSDRGTE FTNDQIEEYF ISKGIHHILT
     STQDHAANGR AERYIRTIIT DATTLLRQSN LRVKFWEYAV TSATNIRNYL EHKSTGKLPL
     KAISRQPVTV RLMSFLPFGE KGIIWNHNHK KLKPSGLPSI ILCKDPNSYG YKFFIPSKNK
     IVTSDNYTIP NYTMDGRVRN TQNINKSHQF SSDNDDEEDQ IETVTNLCEA LENYEDDNKP
     ITRLEDLFTE EELSQIDSNA KYPSPSNNLE GDLDYVFSDV EESGDYDVES ELSTTNNSIS
     TDKNKILSNK DFNSELASTE ISISGIDKKG LINTSHIDED KYDEKVHRIP SIIQEKLVGS
     KNTIKINDEN KISDRIRSKN IGSILNTGLS RCVDITDESI TNKDESMHNA KPELIQEQLK
     KTNHETSFPK EGSIGTNVKF RNTNNEISLK TGDTSLPIKT LESINNHHSN DYSTNKVEKF
     EKENHHPPPI EDIVDMSDQT DMESNCQDGN NLKELKVTDK NVPTDNGTNV SPRLEQNIEA
     SGSPVQTVNK SAFLNKEFSS LNMKRKRKRH DKNNSLTSYE LERDKKRSKK NRVKLIPDNM
     ETVSAPKIRA IYYNEAISKN PDLKEKHEYK QAYHKELQNL KDMKVFDVDV KYSRSEIPDN
     LIVPTNTIFT KKRNGIYKAR IVCRGDTQSP DTYSVITTES LNHNHIKIFL MIANNRNMFM
     KTLDINHAFL YAKLEEEIYI PHPHDRRCVV KLNKALYGLK QSPKEWNDHL RQYLNGIGLK
     DNSYTPGLYQ TEDKNLMIAV YVDDCVIAAS NEQRLDEFIN KLKSNFELKI TGTLIDDVLD
     TDILGMDLVY NKRLGTIDLT LKSFINRMDK KYNEELKKIR KSSIPHMSTY KIDPKKDVLQ
     MSEEEFRQGV LKLQQLLGEL NYVRHKCRYD IEFAVKKVAR LVNYPHERVF YMIYKIIQYL
     VRYKDIGIHY DRDCNKDKKV IAITDASVGS EYDAQSRIGV ILWYGMNIFN VYSNKSTNRC
     VSSTEAELHA IYEGYADSET LKVTLKELGE GDNNDIVMIT DSKPAIQGLN RSYQQPKEKF
     TWIKTEIIKE KIKEKSIKLL KITGKGNIAD LLTKPVSASD FKRFIQVLKN KITSQDILAS
     TDY
//