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P0C2J7

- YH41B_YEAST

UniProt

P0C2J7 - YH41B_YEAST

Protein

Transposon Ty4-H Gag-Pol polyprotein

Gene

TY4B-H

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 65 (01 Oct 2014)
      Sequence version 1 (06 Mar 2007)
      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 sitei414 – 4141For protease activity; shared with dimeric partnerBy similarity
    Metal bindingi630 – 6301Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi695 – 6951Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi1383 – 13831Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1462 – 14621Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1463 – 14631Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1644 – 16441Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1686 – 16861Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1720 – 17201Magnesium; 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-H 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-H
    Synonyms:YHLWTy4-1 POL
    Ordered Locus Names:YHL009W-B
    ORF Names:YHL008W-A
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VIII

    Organism-specific databases

    SGDiS000007372. YHL009W-B.

    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 – 18021802Transposon Ty4-H Gag-Pol polyproteinPRO_0000279380Add
    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

    PRIDEiP0C2J7.

    Expressioni

    Gene expression databases

    GenevestigatoriP0C2J7.

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    BioGridi36417. 6 interactions.
    STRINGi4932.YHL009W-B.

    Structurei

    3D structure databases

    ProteinModelPortaliP0C2J7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini619 – 786168Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST
    Domaini1375 – 1510136Reverse transcriptase Ty1/copia-typeAdd
    BLAST
    Domaini1644 – 1790147RNase H Ty1/copia-typeAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni381 – 501121Ty4 proteaseAdd
    BLAST
    Regioni539 – 59961Integrase-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

    GeneTreeiENSGT00720000109470.
    HOGENOMiHOG000155565.
    OMAiFERASTY.
    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-H Gag-Pol polyprotein (identifier: P0C2J7-1) [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

    MATPVRDETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVKQ     50
    YQRNLNRFKT ILNGLKAEEE KLSETDDIQM LAEKLLKLGE TIDKVENRIV 100
    DLVEKIQLLE TNENNNILHE HIDATGTYYL FDTLTSTNKR FYPKDCVFDY 150
    RTNNVENIPI LLNNFKKFIK KYQFDDVFEN DIIEIDPREN EILCKIIKEG 200
    LGESLDIMNT NTTDIFRIID GLKNKYRSLH GRDVRIRAWE KVLVDTTCRN 250
    SALLMNKLQK LVLMEKWIFS KCCQDCPNLK DYLQEAIMGT LHESLRNSVK 300
    QRLYNIPHNV GINHEEFLIN TVIETVIDLS PIADDQIENS CMYCKSVFHC 350
    SINCKKKPNR ELGLTRPISQ KPIIYKVHRD NNNLSPVQNE QKSWNKTQKK 400
    SNKVYNSKKL VIIDTGSGVN ITNDKTLLHN YEDSNRSTRF FGIGKNSSVS 450
    VKGYGYIKIK NGHNNTDNKC LLTYYVPEEE STIISCYDLA KKTKMVLSRK 500
    YTRLGNKIIK IKTKIVNGVI HVKMNELIER PSDDSKINAI KPTSSPGFKL 550
    NKRSITLEDA HKRMGHTGIQ QIENSIKHNH YEESLDLIKE PNEFWCQTCK 600
    ISKATKRNHY TGSMNNHSTD HEPGSSWCMD IFGPVSSSNA DTKRYMLIMV 650
    DNNTRYCMTS THFNKNAETI LAQIRKNIQY VETQFDRKVR EINSDRGTEF 700
    TNDQIEEYFI SKGIHHILTS TQDHAANGRA ERYIRTIVTD ATTLLRQSNL 750
    RVKFWEYAVT SATNIRNCLE HKSTGKLPLK AISRQPVTVR LMSFLPFGEK 800
    GIIWNHNHKK LKPSGLPSII LCKDPNSYGY KFFIPSKNKI VTSDNYTIPN 850
    YTMDGRVRNT QNIYKSHQFS SHNDNEEDQI ETVTNLCEAL ENYEDDNKPI 900
    TRLEDLFTEE ELSQIDSNAK YPSPSNNLEG DLDYVFSDVE ESGDYDVESE 950
    LSTTNTSIST DKNKILSNKD FNSELASTEI SISEIDKKGL INTSHIDEDK 1000
    YDEKVHRIPS IIQEKLVGSK NTIKINDENR ISDRIRSKNI GSILNTGLSR 1050
    CVDITDESIT NKDESMHNAK PELIQEQFNK TNHETSFPKE GSIGTNVKFR 1100
    NTDNEISLKT GDTSLPIKTL ESINNHHSND YSTNKVEKFE KENHHPPPIE 1150
    DIVDMSDQTD MESNCQDGNN LKELKVTDKN VPTDNGTNVS PRLEQNIEAS 1200
    GSPVQTVNKS AFLNKEFSSL NMKRKRKRHD KNNSLTSYEL ERDKKRSKRN 1250
    RVKLIPDNME TVSAQKIRAI YYNEAISKNP DLKEKHEYKQ AYHKELQNLK 1300
    DMKVFDVDVK YSRSEIPDNL IVPTNTIFTK KRNGIYKARI VCRGDTQSPD 1350
    TYSVITTESL NHNHIKIFLM IANNRNMFMK TLDINHAFLY AKLEEEIYIP 1400
    HPHDRRCVVK LNKALYGLKQ SPKEWNDHLR QYLNGIGLKD NSYTPGLYQT 1450
    EDKNLMIAVY VDDCVIAASN EQRLDEFINK LKSNFELKIT GTLIDDVLDT 1500
    DILGMDLVYN KRLGTIDLTL KSFINRMDKK YNEELKKIRK SSIPHMSTYK 1550
    IDPKKDVLQM SEEEFRQGVL KLQQLLGELN YVRHKCRYDI NFAVKKVARL 1600
    VNYPHERVFY MIYKIIQYLV RYKDIGIHYD RDCNKDKKVI AITDASVGSE 1650
    YDAQSRIGVI LWYGMNIFNV YSNKSTNRCV SSTEAELHAI YEGYADSETL 1700
    KVTLKELGEG DNNDIVMITD SKPAIQGLNR SYQQPKEKFT WIKTEIIKEK 1750
    IKEKSIKLLK ITGKGNIADL LTKPVSASDF KRFIQVLKNK ITSQDILAST 1800
    DY 1802

    Note: Produced by +1 ribosomal frameshifting between codon Leu-362 and Gly-363 of the YHL009W-A ORF.

    Length:1,802
    Mass (Da):207,970
    Last modified:March 6, 2007 - v1
    Checksum:i7F6A8A3483966588
    GO
    Isoform Transposon Ty4-H Gag polyprotein (identifier: Q6Q5P6-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry Q6Q5P6.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:413
    Mass (Da):48,214
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U11581 Genomic DNA. No translation available.
    BK006934 Genomic DNA. Translation: DAA06678.1.
    PIRiS52611.
    RefSeqiNP_058133.1. NM_001184404.1. [P0C2J7-1]

    Genome annotation databases

    EnsemblFungiiYHL009W-B; YHL009W-B; YHL009W-B. [P0C2J7-1]
    GeneIDi856380.
    KEGGisce:YHL009W-B.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U11581 Genomic DNA. No translation available.
    BK006934 Genomic DNA. Translation: DAA06678.1 .
    PIRi S52611.
    RefSeqi NP_058133.1. NM_001184404.1. [P0C2J7-1 ]

    3D structure databases

    ProteinModelPortali P0C2J7.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36417. 6 interactions.
    STRINGi 4932.YHL009W-B.

    Proteomic databases

    PRIDEi P0C2J7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YHL009W-B ; YHL009W-B ; YHL009W-B . [P0C2J7-1 ]
    GeneIDi 856380.
    KEGGi sce:YHL009W-B.

    Organism-specific databases

    SGDi S000007372. YHL009W-B.

    Phylogenomic databases

    GeneTreei ENSGT00720000109470.
    HOGENOMi HOG000155565.
    OMAi FERASTY.
    OrthoDBi EOG7TJ3S3.

    Miscellaneous databases

    NextBioi 981875.

    Gene expression databases

    Genevestigatori P0C2J7.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "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.
    4. "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 nameiYH41B_YEAST
    AccessioniPrimary (citable) accession number: P0C2J7
    Secondary accession number(s): D3DKQ5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 6, 2007
    Last sequence update: March 6, 2007
    Last modified: October 1, 2014
    This is version 65 of the entry and version 1 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 VIII
      Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

    External Data

    Dasty 3