YJ41B_YEAST
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 03-AUG-2022, entry version 136.
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; 19.
DR IntAct; P47024; 6.
DR MINT; P47024; -.
DR PRIDE; P47024; -.
DR GeneID; 853330; -.
DR KEGG; sce:YJL113W; -.
DR SGD; S000003649; YJL113W.
DR InParanoid; P47024; -.
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: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:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0032197; P:transposition, RNA-mediated; ISS:SGD.
DR Gene3D; 3.30.420.10; -; 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 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 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
