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O13535

- YH11B_YEAST

UniProt

O13535 - YH11B_YEAST

Protein

Transposon Ty1-H Gag-Pol polyprotein

Gene

TY1B-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 103 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      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. The particles are assembled from trimer-clustered units and there are holes in the capsid shells that allow for the diffusion of macromolecules. CA has also nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty1 RNA and initiation of reverse transcription By similarity.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
    Sitei439 – 4402Cleavage; by Ty1 proteaseBy similarity
    Active sitei499 – 4991For protease activity; shared with dimeric partnerPROSITE-ProRule annotation
    Sitei620 – 6212Cleavage; by Ty1 proteaseBy similarity
    Metal bindingi709 – 7091Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi774 – 7741Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Sitei1255 – 12562Cleavage; by Ty1 proteaseBy similarity
    Metal bindingi1384 – 13841Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1465 – 14651Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1466 – 14661Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1648 – 16481Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1690 – 16901Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1723 – 17231Magnesium; 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. metal ion binding Source: UniProtKB-KW
    6. peptidase activity Source: SGD
    7. ribonuclease activity Source: SGD
    8. RNA binding Source: SGD
    9. RNA-directed DNA polymerase activity Source: SGD
    10. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

    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 Ty1-H Gag-Pol polyprotein
    Alternative name(s):
    Gag-Pol-p199
    TY1A-TY1B
    Transposon Ty1 TYA-TYB polyprotein
    p190
    Cleaved into the following 4 chains:
    Capsid protein
    Short name:
    CA
    Alternative name(s):
    Gag-p45
    p54
    Ty1 protease (EC:3.4.23.-)
    Short name:
    PR
    Alternative name(s):
    Pol-p20
    p23
    Integrase
    Short name:
    IN
    Alternative name(s):
    Pol-p71
    p84
    p90
    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
    Alternative name(s):
    Pol-p63
    p60
    Gene namesi
    Name:TY1B-H
    Synonyms:YHRCTy1-1 POL
    Ordered Locus Names:YHR214C-B
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VIII

    Organism-specific databases

    CYGDiYHR214c-b.
    SGDiS000003534. YHR214C-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 – 17931793Transposon Ty1-H Gag-Pol polyproteinPRO_0000279074Add
    BLAST
    Chaini1 – 439439Capsid proteinBy similarityPRO_0000279075Add
    BLAST
    Chaini440 – 620181Ty1 proteaseBy similarityPRO_0000279076Add
    BLAST
    Chaini621 – 1255635IntegraseBy similarityPRO_0000279077Add
    BLAST
    Chaini1256 – 1793538Reverse transcriptase/ribonuclease HBy similarityPRO_0000279078Add
    BLAST

    Post-translational modificationi

    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 yielding capsid protein p45 and a Pol-p154 precursor protein. This cleavage is a prerequisite for subsequent processing of Pol-p154 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 similarity

    Expressioni

    Gene expression databases

    GenevestigatoriO13535.

    Interactioni

    Subunit structurei

    The capsid protein forms a homotrimer, from which the VLPs are assembled. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues By similarity.By similarity

    Protein-protein interaction databases

    BioGridi36648. 7 interactions.
    IntActiO13535. 3 interactions.
    MINTiMINT-7544181.
    STRINGi4932.YHR214C-B.

    Structurei

    3D structure databases

    ProteinModelPortaliO13535.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini698 – 873176Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST
    Domaini1376 – 1514139Reverse transcriptase Ty1/copia-typeAdd
    BLAST
    Domaini1648 – 1790143RNase H Ty1/copia-typeAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni337 – 439103RNA-bindingBy similarityAdd
    BLAST
    Regioni621 – 67858Integrase-type zinc finger-likeAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1216 – 125035Bipartite nuclear localization signalBy similarityAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi72 – 14675Pro-richAdd
    BLAST

    Domaini

    The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities.By similarity
    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
    Contains 1 peptidase A11 domain.Curated

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    GeneTreeiENSGT00730000111405.
    HOGENOMiHOG000280731.
    OrthoDBiEOG7TJ3S3.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    InterProiIPR001969. Aspartic_peptidase_AS.
    IPR001584. Integrase_cat-core.
    IPR015820. Retrotransposon_Ty1A_N.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    [Graphical view]
    PfamiPF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    PF01021. TYA. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    PROSITEiPS00141. ASP_PROTEASE. 1 hit.
    PS50994. INTEGRASE. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

    Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift. The ratio of Gag:Gag-Pol varies between 20:1 and 5:1 (By similarity).By similarity

    Isoform Transposon Ty1-H Gag-Pol polyprotein (identifier: O13535-1) [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

    MESQQLSNYP HISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA     50
    NSQQTTTPAS SAVPENLHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG 100
    WSFYGHPSMI PYTPYQMSPM YFPPGPQSQF PQYPSSVGTP LSTPSPESGN 150
    TFTDSSSADS DMTSTKKYVR PPPMLTSPND FPNWVKTYIK FLQNSNLGGI 200
    IPTVNGKPVP PMLTSPNDFP NWVKTYIKFL QNSNLGGIIP TVNGKPVRQI 250
    TDDELTFLYN TFQIFAPSQF LPTWVKDILS VDYTDIMKIL SKSIEKMQSD 300
    TQEANDIVTL ANLQYNGSTP ADAFETKVTN IIDRLNNNGI HINNKVACQL 350
    IMRGLSGEYK FLRYTRHRHL NMTVAELFLD IHAIYEEQQG SRNSKPNYRR 400
    NPSDEKNDSR SYTNTTKPKV IARNPQKTNN SKSKTARAHN VSTSNNSPST 450
    DNDSISKSTT EPIQLNNKHD LHLGQKLTES TVNHTNHSDD ELPGHLLLDS 500
    GASRTLIRSA HHIHSASSNP DINVVDAQKR NIPINAIGDL QFHFQDNTKT 550
    SIKVLHTPNI AYDLLSLNEL AAVDITACFT KNVLERSDGT VLAPIVKYGD 600
    FYWVSKKYLL PSNISVPTIN NVHTSESTRK YPYPFIHRML AHANAQTIRY 650
    SLKNNTITYF NESDVDWSSA IDYQCPDCLI GKSTKHRHIK GSRLKYQNSY 700
    EPFQYLHTDI FGPVHNLPKS APSYFISFTD ETTKFRWVYP LHDRREDSIL 750
    DVFTTILAFI KNQFQASVLV IQMDRGSEYT NRTLHKFLEK NGITPCYTTT 800
    ADSRAHGVAE RLNRTLLDDC RTQLQCSGLP NHLWFSAIEF STIVRNSLAS 850
    PKSKKSARQH AGLAGLDIST LLPFGQPVIV NDHNPNSKIH PRGIPGYALH 900
    PSRNSYGYII YLPSLKKTVD TTNYVILQGK ESRLDQFNYD ALTFDEDLNR 950
    LTASYHSFIA SNEIQQSNDL NIESDHDFQS DIELHPEQLR NVLSKAVSPT 1000
    DSTPPSTHTE DSKRVSKTNI RAPREVDPNI SESNILPSKK RSSTPQISDI 1050
    ESTGSGGMHR LDVPLLAPMS QSNTHESSHA SKSKDFRHSD SYSDNETNHT 1100
    NVPISSTGGT NNKTVPQTSE QETEKRIIHR SPSIDTSSSE SNSLHHVVPI 1150
    KTSDTCPKEN TEESIIADLP LPDLPPEPPT ELSDSFKELP PINSHQTNSS 1200
    LGGIGDSNAY TTINSKKRSL EDNETEIKVS RDTWNTKNMR SLEPPRSKKR 1250
    IHLIAAVKAV KSIKPIRTTL RYDEAITYNK DIKEKEKYIQ AYHKEVNQLL 1300
    MMKTWDTDRY YDRKEIDPKR VINSMFIFNR KRDGTHKARF VARGDIQHPD 1350
    TYDPGMQSNT VHHYALMTSL SLALDNNYYI TQLDISSAYL YADIKEELYI 1400
    RPPPHLGMND KLIRLKKSLY GLKQSGANWY ETIKSYLIKQ CGMEEVRGWS 1450
    CVFKNSQVTI CLFVDDMILF SKDLNANKKI ITTLKKQYDT KIINLGESDN 1500
    EIQYDILGLE IKYQRGKYMK LGMENSLTEK IPKLNVPLNP KGRKLSAPGQ 1550
    PGLYIDQDEL EIDEDEYKEK VHEMQKLIGL ASYVGYKFRF DLLYYINTLA 1600
    QHILFPSRQV LDMTYELIQF MWDTRDKQLI WHKNKPTEPD NKLVAISDAS 1650
    YGNQPYYKSQ IGNIYLLNGK VIGGKSTKAS LTCTSTTEAE IHAISESVPL 1700
    LNNLSHLVQE LNKKPITKGL LTDSKSTISI IISNNEEKFR NRFFGTKAMR 1750
    LRDEVSGNHL HVCYIETKKN IADVMTKPLP IKTFKLLTNK WIH 1793

    Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YHR214C-C ORF.

    Length:1,793
    Mass (Da):202,817
    Last modified:January 1, 1998 - v1
    Checksum:i1DA6A07E10E0A2CB
    GO
    Isoform Transposon Ty1-H Gag polyprotein (identifier: P0C2I4-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry P0C2I4.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:478
    Mass (Da):53,325
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00029 Genomic DNA. Translation: AAB69744.1.
    BK006934 Genomic DNA. Translation: DAA06910.1.
    PIRiS40969.
    S52601.
    RefSeqiNP_012086.1. NM_001181431.1. [O13535-1]

    Genome annotation databases

    EnsemblFungiiYHR214C-B; YHR214C-B; YHR214C-B. [O13535-1]
    GeneIDi856623.
    KEGGisce:YHR214C-B.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00029 Genomic DNA. Translation: AAB69744.1 .
    BK006934 Genomic DNA. Translation: DAA06910.1 .
    PIRi S40969.
    S52601.
    RefSeqi NP_012086.1. NM_001181431.1. [O13535-1 ]

    3D structure databases

    ProteinModelPortali O13535.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36648. 7 interactions.
    IntActi O13535. 3 interactions.
    MINTi MINT-7544181.
    STRINGi 4932.YHR214C-B.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YHR214C-B ; YHR214C-B ; YHR214C-B . [O13535-1 ]
    GeneIDi 856623.
    KEGGi sce:YHR214C-B.

    Organism-specific databases

    CYGDi YHR214c-b.
    SGDi S000003534. YHR214C-B.

    Phylogenomic databases

    GeneTreei ENSGT00730000111405.
    HOGENOMi HOG000280731.
    OrthoDBi EOG7TJ3S3.

    Miscellaneous databases

    NextBioi 982559.

    Gene expression databases

    Genevestigatori O13535.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    InterProi IPR001969. Aspartic_peptidase_AS.
    IPR001584. Integrase_cat-core.
    IPR015820. Retrotransposon_Ty1A_N.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    [Graphical view ]
    Pfami PF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    PF01021. TYA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    PROSITEi PS00141. ASP_PROTEASE. 1 hit.
    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.
    5. "Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1 element."
      Wilhelm F.-X., Wilhelm M., Gabriel A.
      Cytogenet. Genome Res. 110:269-287(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW, DOMAINS.

    Entry informationi

    Entry nameiYH11B_YEAST
    AccessioniPrimary (citable) accession number: O13535
    Secondary accession number(s): D3DLG6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 6, 2007
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 103 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. Ty1 retrotransposons belong to the copia elements (pseudoviridae).

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

    Documents

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

    External Data

    Dasty 3