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P47024

- YJ41B_YEAST

UniProt

P47024 - YJ41B_YEAST

Protein

Transposon Ty4-J Gag-Pol polyprotein

Gene

TY4B-J

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 3 (02 Nov 2010)
      Previous versions | rss
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    Functioni

    Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome.By similarity
    The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.By similarity
    Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends By similarity.By similarity
    Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome By similarity.By similarity

    Catalytic activityi

    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    Endonucleolytic cleavage to 5'-phosphomonoester.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei415 – 4151For protease activity; shared with dimeric partnerBy similarity
    Metal bindingi631 – 6311Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi696 – 6961Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi1384 – 13841Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1463 – 14631Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1464 – 14641Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1645 – 16451Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1687 – 16871Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1721 – 17211Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: UniProtKB-KW
    2. ATP binding Source: UniProtKB-KW
    3. DNA binding Source: UniProtKB-KW
    4. DNA-directed DNA polymerase activity Source: SGD
    5. peptidase activity Source: SGD
    6. ribonuclease activity Source: SGD
    7. RNA binding Source: SGD
    8. RNA-directed DNA polymerase activity Source: SGD
    9. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC
    10. zinc ion binding Source: InterPro

    GO - Biological processi

    1. DNA-dependent DNA replication Source: GOC
    2. DNA integration Source: UniProtKB-KW
    3. DNA recombination Source: UniProtKB-KW
    4. RNA-dependent DNA replication Source: GOC
    5. RNA phosphodiester bond hydrolysis Source: GOC
    6. transposition, RNA-mediated Source: SGD
    7. viral release from host cell Source: UniProtKB-KW

    Keywords - Molecular functioni

    Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

    Keywords - Biological processi

    DNA integration, DNA recombination, Transposition, Virion maturation, Virus exit from host cell

    Keywords - Ligandi

    ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Transposon Ty4-J Gag-Pol polyprotein
    Alternative name(s):
    TY4A-TY4B
    Transposon Ty4 TYA-TYB polyprotein
    Including the following 4 domains:
    Capsid protein
    Short name:
    CA
    Ty4 protease (EC:3.4.23.-)
    Short name:
    PR
    Integrase
    Short name:
    IN
    Reverse transcriptase/ribonuclease H (EC:2.7.7.49, EC:2.7.7.7, EC:3.1.26.4)
    Short name:
    RT
    Short name:
    RT-RH
    Gene namesi
    Name:TY4B-J
    Synonyms:YJLWTy4-1 POL
    Ordered Locus Names:YJL113W
    ORF Names:J0780
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome X

    Organism-specific databases

    SGDiS000003649. YJL113W.

    Subcellular locationi

    Cytoplasm. Nucleus By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleus Source: SGD
    3. retrotransposon nucleocapsid Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 18031803Transposon Ty4-J Gag-Pol polyproteinPRO_0000203502Add
    BLAST

    Post-translational modificationi

    Proteolytically processed into capsid protein (CA), Ty4 protease (PR), integrase (IN) and reverse transcriptase/ribonuclease H (RT) proteins Probable. Initially, virus-like particles (VLPs) are composed of the structural unprocessed proteins Gag and Gag-Pol, and contain also the host initiator methionine tRNA (tRNA(i)-Met) which serves as a primer for minus-strand DNA synthesis, and a dimer of genomic Ty RNA. Processing of the polyproteins occurs within the particle and proceeds by an ordered pathway, called maturation. First, the protease (PR) is released by autocatalytic cleavage of the Gag-Pol polyprotein, and this cleavage is a prerequisite for subsequent processing at the remaining sites to release the mature structural and catalytic proteins. Maturation takes place prior to the RT reaction and is required to produce transposition-competent VLPs By similarity.By similarityCurated

    Proteomic databases

    PaxDbiP47024.

    Expressioni

    Gene expression databases

    GenevestigatoriP47024.

    Interactioni

    Subunit structurei

    The protease is a homodimer, whose active site consists of two apposed aspartic acid residues.By similarity

    Protein-protein interaction databases

    BioGridi33642. 19 interactions.
    IntActiP47024. 6 interactions.
    MINTiMINT-436711.
    STRINGi4932.YJL113W.

    Structurei

    3D structure databases

    ProteinModelPortaliP47024.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini620 – 787168Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST
    Domaini1376 – 1511136Reverse transcriptase Ty1/copia-typeAdd
    BLAST
    Domaini1645 – 1791147RNase H Ty1/copia-typeAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni382 – 502121Ty4 proteaseAdd
    BLAST
    Regioni540 – 60061Integrase-type zinc finger-likeAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili39 – 11577Sequence AnalysisAdd
    BLAST

    Domaini

    Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.By similarity

    Sequence similaritiesi

    Contains 1 integrase catalytic domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Coiled coil, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG283194.
    HOGENOMiHOG000155565.
    OrthoDBiEOG7TJ3S3.

    Family and domain databases

    Gene3Di3.30.420.10. 2 hits.
    InterProiIPR001584. Integrase_cat-core.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    IPR001878. Znf_CCHC.
    [Graphical view]
    PfamiPF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    [Graphical view]
    SMARTiSM00343. ZnF_C2HC. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    PROSITEiPS50994. INTEGRASE. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

    Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift.

    Isoform Transposon Ty4-J Gag-Pol polyprotein (identifier: P47024-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MATPVRGETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVRQ     50
    YQRNLNRFKT ILNGLKAEEE KLSEADDIQM LAEKLLKLGE TIDKVENRIV 100
    DLVEKIQLLE TNENNNILHE HIDATGTYYL FDTLTSTNKR FYPKDCVFDY 150
    RTNNVENIPI LLNNFKKFIK KYQFDDVFEN DIIEIDPREN EILCKIIKEG 200
    LGESLDIMNT NTTDIFRIID GLKKQNIEVC MVEMSELEPG EKVLVDTTCR 250
    NSALLMNKLQ KLVLMEKWIF SKCCQDCPNL KDYLQEAIMG TLHESLRNSV 300
    KQRLYNIPHD VGIDHEEFLI NTVIETVIDL SPIADDQIEN SCMYCKSVFH 350
    CSINCKKKPN RELGLTRPIS QKPIIYKVHR DNNHLSPVQN EQKSWNKTQK 400
    RSNKVYNSKK LVIIDTGSGV NITNDKTLLH NYEDSNRSTR FFGIGKNSSV 450
    SVKGYGYIKI KNGHNNTDNK CLLTYYVPEE ESTIISCYDL AKKTKMVLSR 500
    KYTRLGNKII KIKTKIVNGV IHVKMNELIE RPSDDSKINA IKPTSSPGFK 550
    LNKRSITLED AHKRMGHTGI QQIENSIKHN HYEESLDLIK EPNEFWCQTC 600
    KISKATKRNH YTGSMNNHST DHEPGSSWCM DIFGPVSSSN ADTKRYMLIM 650
    VDNNTRYCMT STHFNKNAET ILAQVRKNIQ YVETQFDRKV REINSDRGTE 700
    FTNDQIEEYF ISKGIHHILT STQDHAANGR AERYIRTIIT DATTLLRQSN 750
    LRVKFWEYAV TSATNIRNYL EHKSTGKLPL KAISRQPVTV RLMSFLPFGE 800
    KGIIWNHNHK KLKPSGLPSI ILCKDPNSYG YKFFIPSKNK IVTSDNYTIP 850
    NYTMDGRVRN TQNINKSHQF SSDNDDEEDQ IETVTNLCEA LENYEDDNKP 900
    ITRLEDLFTE EELSQIDSNA KYPSPSNNLE GDLDYVFSDV EESGDYDVES 950
    ELSTTNNSIS TDKNKILSNK DFNSELASTE ISISGIDKKG LINTSHIDED 1000
    KYDEKVHRIP SIIQEKLVGS KNTIKINDEN KISDRIRSKN IGSILNTGLS 1050
    RCVDITDESI TNKDESMHNA KPELIQEQLK KTNHETSFPK EGSIGTNVKF 1100
    RNTNNEISLK TGDTSLPIKT LESINNHHSN DYSTNKVEKF EKENHHPPPI 1150
    EDIVDMSDQT DMESNCQDGN NLKELKVTDK NVPTDNGTNV SPRLEQNIEA 1200
    SGSPVQTVNK SAFLNKEFSS LNMKRKRKRH DKNNSLTSYE LERDKKRSKK 1250
    NRVKLIPDNM ETVSAPKIRA IYYNEAISKN PDLKEKHEYK QAYHKELQNL 1300
    KDMKVFDVDV KYSRSEIPDN LIVPTNTIFT KKRNGIYKAR IVCRGDTQSP 1350
    DTYSVITTES LNHNHIKIFL MIANNRNMFM KTLDINHAFL YAKLEEEIYI 1400
    PHPHDRRCVV KLNKALYGLK QSPKEWNDHL RQYLNGIGLK DNSYTPGLYQ 1450
    TEDKNLMIAV YVDDCVIAAS NEQRLDEFIN KLKSNFELKI TGTLIDDVLD 1500
    TDILGMDLVY NKRLGTIDLT LKSFINRMDK KYNEELKKIR KSSIPHMSTY 1550
    KIDPKKDVLQ MSEEEFRQGV LKLQQLLGEL NYVRHKCRYD IEFAVKKVAR 1600
    LVNYPHERVF YMIYKIIQYL VRYKDIGIHY DRDCNKDKKV IAITDASVGS 1650
    EYDAQSRIGV ILWYGMNIFN VYSNKSTNRC VSSTEAELHA IYEGYADSET 1700
    LKVTLKELGE GDNNDIVMIT DSKPAIQGLN RSYQQPKEKF TWIKTEIIKE 1750
    KIKEKSIKLL KITGKGNIAD LLTKPVSASD FKRFIQVLKN KITSQDILAS 1800
    TDY 1803

    Note: Produced by +1 ribosomal frameshifting between codon Leu-363 and Gly-364 of the YJL114W ORF.

    Length:1,803
    Mass (Da):207,710
    Last modified:November 2, 2010 - v3
    Checksum:iA58D1D4E96F7C9C9
    GO
    Isoform Transposon Ty4-J Gag polyprotein (identifier: P47023-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry P47023.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:414
    Mass (Da):48,035
    GO

    Sequence cautioni

    The sequence DAA08686.2 differs from that shown. Reason: Frameshift at positions 226 and 240.
    The sequence CAA89409.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti452 – 4521V → L in X67284. (PubMed:1328182)Curated
    Sequence conflicti684 – 6841T → A in X67284. (PubMed:1328182)Curated
    Sequence conflicti920 – 9201A → S in X67284. (PubMed:1328182)Curated
    Sequence conflicti1020 – 10201S → R in X67284. (PubMed:1328182)Curated
    Sequence conflicti1803 – 18031Y → YLINEVLNTQISVEVQ in X67284. (PubMed:1328182)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X67284 Genomic DNA. No translation available.
    Z49389 Genomic DNA. Translation: CAA89409.1. Sequence problems.
    BK006943 Genomic DNA. Translation: DAA08686.2. Frameshift.
    PIRiS31262.
    S56894.
    RefSeqiNP_012421.2. NM_001181546.2.

    Genome annotation databases

    GeneIDi853330.
    KEGGisce:YJL113W.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X67284 Genomic DNA. No translation available.
    Z49389 Genomic DNA. Translation: CAA89409.1 . Sequence problems.
    BK006943 Genomic DNA. Translation: DAA08686.2 . Frameshift.
    PIRi S31262.
    S56894.
    RefSeqi NP_012421.2. NM_001181546.2.

    3D structure databases

    ProteinModelPortali P47024.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33642. 19 interactions.
    IntActi P47024. 6 interactions.
    MINTi MINT-436711.
    STRINGi 4932.YJL113W.

    Proteomic databases

    PaxDbi P47024.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 853330.
    KEGGi sce:YJL113W.

    Organism-specific databases

    SGDi S000003649. YJL113W.

    Phylogenomic databases

    eggNOGi NOG283194.
    HOGENOMi HOG000155565.
    OrthoDBi EOG7TJ3S3.

    Miscellaneous databases

    NextBioi 973695.

    Gene expression databases

    Genevestigatori P47024.

    Family and domain databases

    Gene3Di 3.30.420.10. 2 hits.
    InterProi IPR001584. Integrase_cat-core.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    IPR001878. Znf_CCHC.
    [Graphical view ]
    Pfami PF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    [Graphical view ]
    SMARTi SM00343. ZnF_C2HC. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    PROSITEi PS50994. INTEGRASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Ty4, a new retrotransposon from Saccharomyces cerevisiae, flanked by tau-elements."
      Janetzky B., Lehle L.
      J. Biol. Chem. 267:19798-19805(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon."
      Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C.
      Yeast 12:1471-1474(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    3. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
      Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 226 AND 240.
      Strain: ATCC 204508 / S288c.
    5. "Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence."
      Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.
      Genome Res. 8:464-478(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NOMENCLATURE.
    6. "Happy together: the life and times of Ty retrotransposons and their hosts."
      Lesage P., Todeschini A.L.
      Cytogenet. Genome Res. 110:70-90(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.

    Entry informationi

    Entry nameiYJ41B_YEAST
    AccessioniPrimary (citable) accession number: P47024
    Secondary accession number(s): D6VW70, P87192
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: November 2, 2010
    Last modified: October 1, 2014
    This is version 95 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Retrotransposons are mobile genetic entities that are able to replicate via an RNA intermediate and a reverse transcription step. In contrast to retroviruses, retrotransposons are non-infectious, lack an envelope and remain intracellular. Ty4 retrotransposons belong to the copia elements (pseudoviridae).

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome X
      Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

    External Data

    Dasty 3