YA11B_YEAST
ID YA11B_YEAST Reviewed; 1196 AA.
AC O13527; D6VPM1;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 02-NOV-2010, sequence version 3.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Truncated transposon Ty1-A Gag-Pol polyprotein;
DE AltName: Full=TY1B;
DE AltName: Full=Transposon Ty1 TYB polyprotein;
DE Contains:
DE RecName: Full=Integrase;
DE Short=IN;
DE AltName: Full=Pol-p71;
DE AltName: Full=p84;
DE AltName: Full=p90;
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;
DE AltName: Full=Pol-p63;
DE AltName: Full=p60;
GN Name=TY1B-A; Synonyms=YARCTy1-1 POL; OrderedLocusNames=YAR009C;
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 204511 / S288c / AB972;
RX PubMed=7941740; DOI=10.1002/yea.320100413;
RA Clark M.W., Keng T., Storms R.K., Zhong W.-W., Fortin N., Zeng B.,
RA Delaney S., Ouellette B.F.F., Barton A.B., Kaback D.B., Bussey H.;
RT "Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42
RT kbp SPO7-CENI-CDC15 region.";
RL Yeast 10:535-541(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7731988; DOI=10.1073/pnas.92.9.3809;
RA Bussey H., Kaback D.B., Zhong W.-W., Vo D.H., Clark M.W., Fortin N.,
RA Hall J., Ouellette B.F.F., Keng T., Barton A.B., Su Y., Davies C.J.,
RA Storms R.K.;
RT "The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995).
RN [3]
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 [4]
RP NOMENCLATURE, AND IDENTIFICATION OF FRAMESHIFT.
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).
RN [6]
RP REVIEW, AND DOMAINS.
RX PubMed=16093680; DOI=10.1159/000084960;
RA Wilhelm F.-X., Wilhelm M., Gabriel A.;
RT "Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1
RT element.";
RL Cytogenet. Genome Res. 110:269-287(2005).
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 -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus {ECO:0000250}.
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 yielding
CC capsid protein p45 and a Pol-p154 precursor protein. This cleavage is a
CC prerequisite for subsequent processing of Pol-p154 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. Ty1 retrotransposons belong
CC to the copia elements (pseudoviridae).
CC -!- CAUTION: Transposon Ty1-A (YARCTy1-1) contains a frameshift at position
CC 610, which disrupts the ORF coding for protein TY1B. This is the
CC truncated, C-terminal part of TY1B translated from an in-frame start
CC codon, and it is probably not functional. {ECO:0000305}.
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DR EMBL; L22015; AAC04967.1; -; Genomic_DNA.
DR EMBL; BK006935; DAA06991.1; -; Genomic_DNA.
DR PIR; S40908; S40908.
DR RefSeq; NP_009406.1; NM_001178213.1.
DR AlphaFoldDB; O13527; -.
DR BioGRID; 31795; 7.
DR DIP; DIP-2632N; -.
DR IntAct; O13527; 3.
DR MINT; O13527; -.
DR STRING; 4932.YAR009C; -.
DR iPTMnet; O13527; -.
DR PaxDb; O13527; -.
DR GeneID; 851268; -.
DR KEGG; sce:YAR009C; -.
DR SGD; S000000067; YAR009C.
DR VEuPathDB; FungiDB:YAR009C; -.
DR eggNOG; KOG0017; Eukaryota.
DR HOGENOM; CLU_003908_0_0_1; -.
DR InParanoid; O13527; -.
DR OMA; TITQEMA; -.
DR PRO; PR:O13527; -.
DR Proteomes; UP000002311; Chromosome I.
DR RNAct; O13527; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0000943; C:retrotransposon nucleocapsid; ISS:SGD.
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:0004540; F:ribonuclease activity; ISS:SGD.
DR GO; GO:0003723; F:RNA binding; 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:0032197; P:transposition, RNA-mediated; ISS:SGD.
DR Gene3D; 3.30.420.10; -; 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 Pfam; PF00665; rve; 1.
DR Pfam; PF07727; RVT_2; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
PE 3: Inferred from homology;
KW Cytoplasm; DNA integration; DNA recombination; DNA-binding;
KW DNA-directed DNA polymerase; Endonuclease; Hydrolase; Magnesium;
KW Metal-binding; Multifunctional enzyme; Nuclease; Nucleotidyltransferase;
KW Nucleus; Reference proteome; RNA-binding; RNA-directed DNA polymerase;
KW Transferase; Transposable element; Transposition.
FT CHAIN 1..1196
FT /note="Truncated transposon Ty1-A Gag-Pol polyprotein"
FT /id="PRO_0000278977"
FT CHAIN 1..658
FT /note="Integrase"
FT /evidence="ECO:0000250"
FT /id="PRO_0000278980"
FT CHAIN 659..1196
FT /note="Reverse transcriptase/ribonuclease H"
FT /evidence="ECO:0000250"
FT /id="PRO_0000278981"
FT DOMAIN 101..276
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT DOMAIN 779..917
FT /note="Reverse transcriptase Ty1/copia-type"
FT DOMAIN 1051..1193
FT /note="RNase H Ty1/copia-type"
FT REGION 397..528
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 533..552
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 571..628
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 619..653
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000250"
FT COMPBIAS 410..424
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 434..459
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 481..497
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 498..521
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 538..552
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 575..589
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 594..619
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 112
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 177
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 787
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 868
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 869
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 1051
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 1093
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 1126
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 658..659
FT /note="Cleavage; by Ty1 protease"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1196 AA; 136732 MW; 0A3E8CFC5B12C6A2 CRC64;
METFTGYLKS TCFHQISPYP PSIMSIQVKV HANILILSFI ECLRMPMHRQ IRYSLKNNTI
TYFNESDVDW SSAIDYQCPD CLIGKSTKHR HIKGSRLKYQ NSYEPFQYLH TDIFGPVHNL
PKSAPSYFIS FTDETTKLRW VYPLHDRRED SILDVFTTIL AFIKNQFQAS VLVIQMDRGS
EYTNRTLHKF LEKNGITPCY TTTADSRAHG VAERLNRTLL DDCRTQLQCS GLPNHLWFSA
IEFSTIVRNS LASPKSKKSA RQHAGLAGLD ISTLLPFGQP VIVNDHNPNS KIHPRGIPGY
ALHPSRNSYG YIIYLPSLKK TVDTTNYVIL QGKESRLDQF NYDALTFDED LNRLTASYHS
FIASNEIQES NDLNIESDHD FQSDIELHPE QPRNVLSKAV SPTDSTPPST HTEDSKRVSK
TNIRAPREVD PNISESNILP SKKRSSTPQI SNIESTGSGG MHKLNVPLLA PMSQSNTHES
SHASKSKDFR HSDSYSENET NHTNVPISST GGTNNKTVPQ ISDQETEKRI IHRSPSIDAS
PPENNSSHNI VPIKTPTTVS EQNTEESIIA DLPLPDLPPE SPTEFPDPFK ELPPINSHQT
NSSLGGIGDS NAYTTINSKK RSLEDNETEI KVSRDTWNTK NMRSLEPPRS KKRIHLIAAV
KAVKSIKPIR TTLRYDEAIT YNKDIKEKEK YIEAYHKEVN QLLKMNTWDT DKYYDRKEID
PKRVINSMFI FNKKRDGTHK ARFVARGDIQ HPDTYDTGMQ SNTVHHYALM TSLSLALDNN
YYITQLDISS AYLYADIKEE LYIRPPPHLG MNDKLIRLKK SLYGLKQSGA NWYETIKSYL
IKQCGMEEVR GWSCVFKNSQ VTICLFVDDM ILFSKDLNAN KKIITTLKKQ YDTKIINLGE
SDNEIQYDIL GLEIKYQRGK YMKLGMEKSL TEKLPKLNVP LNPKGKKLRA PGQPGLYIDQ
DELEIDEDEY KEKVHEMQKL IGLASYVGYK FRFDLLYYIN TLAQHILFPS RQVLDMTYEL
IQFMWDTRDK QLIWHKNKPT EPDNKLVAIS DASYGNQPYY KSQIGNIYLL NGKVIGGKST
KASLTCTSTT EAEIHAISES VPLLNNLSYL IQELNKKPII KGLLTDSRST ISIIKSTNEE
KFRNRFFGTK AMRLRDEVSG NNLYVYYIET KKNIADVMTK PLPIKTFKLL TNKWIH
