ID   YF21B_YEAST             Reviewed;        1770 AA.
AC   P0CX63; D6VTM7; Q05369; Q12503;
DT   28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 1.
DT   27-MAR-2024, entry version 80.
DE   RecName: Full=Transposon Ty2-F Gag-Pol polyprotein;
DE   AltName: Full=TY2A-TY2B;
DE   AltName: Full=Transposon Ty2 TYA-TYB polyprotein;
DE   Contains:
DE     RecName: Full=Capsid protein;
DE              Short=CA;
DE   Contains:
DE     RecName: Full=Ty2 protease;
DE              Short=PR;
DE              EC=3.4.23.-;
DE   Contains:
DE     RecName: Full=Integrase;
DE              Short=IN;
DE   Contains:
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=TY2B-F; Synonyms=YFLWTy2-1 POL; OrderedLocusNames=YFL002W-A;
GN   ORFNames=FN01;
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=7670463; DOI=10.1038/ng0795-261;
RA   Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S.,
RA   Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H.,
RA   Eki T.;
RT   "Analysis of the nucleotide sequence of chromosome VI from Saccharomyces
RT   cerevisiae.";
RL   Nat. Genet. 10:261-268(1995).
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   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   -!- 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 capsid protein forms a homotrimer, from which the VLPs are
CC       assembled. The protease is a homodimer, whose active site consists of
CC       two apposed aspartic acid residues (By similarity). {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 Ty2-F Gag-Pol polyprotein;
CC         IsoId=P0CX63-1; Sequence=Displayed;
CC       Name=Transposon Ty2-F Gag polyprotein;
CC         IsoId=P0CX61-1; 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   -!- 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: Initially, virus-like particles (VLPs) are composed of the
CC       structural unprocessed proteins Gag and Gag-Pol, and also contain the
CC       host initiator methionine tRNA (tRNA(i)-Met) which serves as a primer
CC       for minus-strand DNA synthesis, and a dimer of genomic Ty RNA.
CC       Processing of the polyproteins occurs within the particle and proceeds
CC       by an ordered pathway, called maturation. First, the protease (PR) is
CC       released by autocatalytic cleavage of the Gag-Pol polyprotein, and this
CC       cleavage is a prerequisite for subsequent processing at the remaining
CC       sites to release the mature structural and catalytic proteins.
CC       Maturation takes place prior to the RT reaction and is required to
CC       produce transposition-competent VLPs (By similarity). {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-F Gag-Pol polyprotein]: Produced
CC       by +1 ribosomal frameshifting between codon Leu-431 and Gly-432 of the
CC       YFL002W-B ORF.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAA09237.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; D50617; BAA09237.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; BK006940; DAA12437.1; -; Genomic_DNA.
DR   PIR; S58651; S58651.
DR   RefSeq; NP_058163.1; NM_001184402.2. [P0CX63-1]
DR   RefSeq; NP_116653.1; NM_001180862.2. [P0CX63-1]
DR   AlphaFoldDB; P0CX63; -.
DR   BioGRID; 31146; 5.
DR   BioGRID; 33410; 4.
DR   MEROPS; A11.003; -.
DR   iPTMnet; P0CX63; -.
DR   PaxDb; 4932-YFL002W-A; -.
DR   PeptideAtlas; P0CX63; -.
DR   GeneID; 850548; -.
DR   GeneID; 853067; -.
DR   KEGG; sce:YFL002W-A; -.
DR   KEGG; sce:YGR161W-B; -.
DR   AGR; SGD:S000002962; -.
DR   SGD; S000002962; YFL002W-A.
DR   VEuPathDB; FungiDB:YFL002W-A; -.
DR   VEuPathDB; FungiDB:YGR161W-B; -.
DR   eggNOG; KOG0017; Eukaryota.
DR   HOGENOM; CLU_244151_0_0_1; -.
DR   InParanoid; P0CX63; -.
DR   OrthoDB; 2039326at2759; -.
DR   Proteomes; UP000002311; Chromosome VI.
DR   RNAct; P0CX63; Protein.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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; 1.
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   InterPro; IPR015820; TYA.
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   Pfam; PF01021; TYA; 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; 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..1770
FT                   /note="Transposon Ty2-F Gag-Pol polyprotein"
FT                   /id="PRO_0000279308"
FT   CHAIN           1..397
FT                   /note="Capsid protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279309"
FT   CHAIN           398..578
FT                   /note="Ty2 protease"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279310"
FT   CHAIN           579..1232
FT                   /note="Integrase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279311"
FT   CHAIN           1233..1770
FT                   /note="Reverse transcriptase/ribonuclease H"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000279312"
FT   DOMAIN          656..831
FT                   /note="Integrase catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   DOMAIN          1353..1491
FT                   /note="Reverse transcriptase Ty1/copia-type"
FT   DOMAIN          1625..1767
FT                   /note="RNase H Ty1/copia-type"
FT   REGION          1..86
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          295..397
FT                   /note="RNA-binding"
FT                   /evidence="ECO:0000250"
FT   REGION          359..453
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          579..636
FT                   /note="Integrase-type zinc finger-like"
FT   REGION          1004..1034
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1059..1135
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1146..1165
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1170..1205
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           1193..1227
FT                   /note="Bipartite nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   COMPBIAS        1..67
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        359..440
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1060..1108
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1170..1187
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1188..1205
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        457
FT                   /note="For protease activity; shared with dimeric partner"
FT                   /evidence="ECO:0000250"
FT   BINDING         667
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         732
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         1361
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         1442
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         1443
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         1625
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         1667
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         1700
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   SITE            397..398
FT                   /note="Cleavage; by Ty2 protease"
FT                   /evidence="ECO:0000250"
FT   SITE            578..579
FT                   /note="Cleavage; by Ty2 protease"
FT                   /evidence="ECO:0000250"
FT   SITE            1232..1233
FT                   /note="Cleavage; by Ty2 protease"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1770 AA;  202039 MW;  97C0C8F7D431D731 CRC64;
     MESQQLHQNP HSLHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV NSQQETTPGT
     SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN WAHYQQPSMM TCSHYQTSPA
     YYQPDPHYPL PQYIPPLSTS SPDPIDSQNQ HSEVPQAETK VRNNVLPPHT LTSEENFSTW
     VKFYIRFLKN SNLGDIIPND QGEIKSQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN
     YADILTVLCK SVSKMQTNNQ ELKDWIALAN LEYDGSTSAD TFEITVSTII QRLKENNINV
     SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN LNKPSQYKQH
     SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA TSSKFSRVNN DHINESTVSS
     QYLSDDNELS LGQQQKESKP THTIDSNDEL PDHLLIDSGA SQTLVRSAHY LHHATPNSEI
     NIVDAQKQDI PINAIGNLHF NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN
     TLERSDGTVL APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH
     ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS RLKYQESYEP
     FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH DRREESILNV FTSILAFIKN
     QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG ITACYTTTAD SRAHGVAERL NRTLLNDCRT
     LLHCSGLPNH LWFSAVEFST IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN
     HNPDSKIHPR GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQDKQS KLDQFNYDTL
     TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND FSSQSINPLQ
     LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE STEMGGTVES DTTSPRHSST
     FTARNQNRPG STNEMIDLTS QDRVNYGLEN IKTTRLGGTE EPYIQRNSDT NIKYRTTNST
     PSIDDRSSNS ESTTPIISIE TKAVCDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD
     SILDDLPLPD LTHKSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN
     ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD EAITYNKDNK
     EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN SMFIFNKKRD GTHKARFVAR
     GDIQHPDTYD SDMQSNTVHH YALMTSLSIA LDNDYYITQL DISSAYLYAD IKEELYIRPP
     PHLGLNDKLL RLRKSLYGLK QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF
     VDDMILFSKD LNANKKIITT LKKQYDTKII NLGESDNEIQ YDILGLEIKY QRSKYMKLGM
     EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE MQKLIGLASY
     VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD TRDKQLIWHK NKPTKPDNKL
     VAISDASYGN QPYYKSQIGN IFLLNGKVIG GKSTKASLTC TSTTEAEIHA VSEAIPLLNN
     LSHLVQELNK KPIIKGLLTD SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY
     YIETKKNIAD VMTKPLPIKT FKLLTNKWIH
//