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Q7LHG5

- YI31B_YEAST

UniProt

Q7LHG5 - YI31B_YEAST

Protein

Transposon Ty3-I Gag-Pol polyprotein

Gene

TY3B-I

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 94 (01 Oct 2014)
      Sequence version 2 (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 genomic RNA-nucleocapsid complex.By similarity
    Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers By similarity. Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 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).PROSITE-ProRule annotation
    Endonucleolytic cleavage to 5'-phosphomonoester.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei207 – 2082Cleavage; by Ty3 protease
    Sitei233 – 2342Cleavage; by Ty3 protease
    Sitei309 – 3102Cleavage; by Ty3 protease
    Active sitei336 – 3361For protease activity; shared with dimeric partnerBy similarity
    Sitei442 – 4432Cleavage; by Ty3 proteaseSequence Analysis
    Sitei561 – 5622Cleavage; by Ty3 protease
    Metal bindingi712 – 7121Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi774 – 7741Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi775 – 7751Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Sitei1037 – 10382Cleavage; by Ty3 protease
    Sitei1063 – 10642Cleavage; by Ty3 protease; partial
    Metal bindingi1201 – 12011Magnesium; catalytic; for integrase activityBy similarity
    Metal bindingi1262 – 12621Magnesium; catalytic; for integrase activityBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri265 – 28218CCHC-typePROSITE-ProRule annotationAdd
    BLAST

    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 phosphodiester bond hydrolysis Source: GOC
    5. transposition, RNA-mediated Source: SGD
    6. 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, 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 Ty3-I Gag-Pol polyprotein
    Alternative name(s):
    Gag3-Pol3
    Transposon Ty3-2 TYA-TYB polyprotein
    Cleaved into the following 8 chains:
    Capsid protein
    Short name:
    CA
    Alternative name(s):
    p24
    Ty3 protease (EC:3.4.23.-)
    Short name:
    PR
    Alternative name(s):
    p16
    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):
    p55
    Integrase p52
    Short name:
    IN
    Integrase p49
    Short name:
    IN
    Gene namesi
    Name:TY3B-I
    Synonyms:YILWTy3-1 POL
    Ordered Locus Names:YIL082W-A
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IX

    Organism-specific databases

    SGDiS000003537. YIL082W-A.

    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 – 14981498Transposon Ty3-I Gag-Pol polyproteinPRO_0000279367Add
    BLAST
    Chaini1 – 207207Capsid proteinPRO_0000279368Add
    BLAST
    Peptidei208 – 23326Spacer peptide p3PRO_0000279369Add
    BLAST
    Chaini234 – 30976Nucleocapsid protein p11PRO_0000279370Add
    BLAST
    Chaini310 – 442133Ty3 proteasePRO_0000279371Add
    BLAST
    Peptidei443 – 561119Spacer peptide JSequence AnalysisPRO_0000279372Add
    BLAST
    Chaini562 – 1037476Reverse transcriptase/ribonuclease HPRO_0000279373Add
    BLAST
    Chaini1038 – 1498461Integrase p52PRO_0000279374Add
    BLAST
    Chaini1064 – 1498435Integrase p49PRO_0000279375Add
    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, 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 similarity

    Expressioni

    Gene expression databases

    GenevestigatoriQ7LHG5.

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    BioGridi34910. 5 interactions.
    IntActiQ7LHG5. 3 interactions.
    MINTiMINT-541560.

    Structurei

    3D structure databases

    ProteinModelPortaliQ7LHG5.
    SMRiQ7LHG5. Positions 576-1037, 1137-1359.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini646 – 823178Reverse transcriptasePROSITE-ProRule annotationAdd
    BLAST
    Domaini919 – 1037119RNase H Ty3/gyspy-typeAdd
    BLAST
    Domaini1185 – 1350166Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1132 – 117140Integrase-type zinc finger-likeAdd
    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 CCHC-type zinc finger.PROSITE-ProRule annotation
    Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
    Contains 1 peptidase A2 domain.Curated
    Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri265 – 28218CCHC-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    HOGENOMiHOG000172599.
    KOiK07497.
    OrthoDBiEOG7HF1TD.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    InterProiIPR001584. Integrase_cat-core.
    IPR024650. Peptidase_A2B.
    IPR021109. Peptidase_aspartic_dom.
    IPR005162. Retrotrans_gag_dom.
    IPR012337. RNaseH-like_dom.
    IPR000477. RT_dom.
    IPR001878. Znf_CCHC.
    [Graphical view]
    PfamiPF12384. Peptidase_A2B. 1 hit.
    PF03732. Retrotrans_gag. 1 hit.
    PF00665. rve. 1 hit.
    PF00078. RVT_1. 1 hit.
    [Graphical view]
    SMARTiSM00343. ZnF_C2HC. 1 hit.
    [Graphical view]
    SUPFAMiSSF50630. SSF50630. 1 hit.
    SSF53098. SSF53098. 1 hit.
    SSF57756. SSF57756. 1 hit.
    PROSITEiPS50994. INTEGRASE. 1 hit.
    PS50878. RT_POL. 1 hit.
    PS50158. ZF_CCHC. 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.

    Isoform Transposon Ty3-I Gag-Pol polyprotein (identifier: Q7LHG5-1) [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

    MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML     50
    NMSMISWPND ASRIVYCRRH LLNPAAQWAN DFVQEQGILE ITFDTFIQGL 100
    YQHFYKPPDI NKIFNAITQL SEAKLGIERL NQRFRKIWDR MPPDFMTEKA 150
    AIMTYTRLLT KETYNIVRMH KPETLKDAME EAYQTTALTE RFFPGFELDA 200
    DGDTIIGATT HLQEEYDSDY DSEDNLTQNR YVHTVRTRRS YNKPMSNHRN 250
    RRNNNASREE CIKNRLCFYC KKEGHRLNEC RARKAVLTDL ELESKDQQTL 300
    FIKTLPIVHY IAIPEMDNTA EKTIKIQNTK VKTLFDSGSP TSFIRRDIVE 350
    LLKYEIYETP PLRFRGFVAT KSAVTSEAVT IDLKINDLQI TLAAYILDNM 400
    DYQLLIGNPI LRRYPKILHT VLNTRESPDS LKPKTYRSET VNNVRTYSAG 450
    NRGNPRNIKL SFAPTILEAT DPKSAGNRGN PRNTKLSLAP TILEATDPKS 500
    AGNRGDSRTK TLSLATTTPA AIDPLTTLDN PGSTQSTFAQ FPIPEEASIL 550
    EEDGKYSNVV STIQSVEPNA TDHSNKDTFC TLPVWLQQKY REIIRNDLPP 600
    RPADINNIPV KHDIEIKPGA RLPRLQPYHV TEKNEQEINK IVQKLLDNKF 650
    IVPSKSPCSS PVVLVPKKDG TFRLCVDYRT LNKATISDPF PLPRIDNLLS 700
    RIGNAQIFTT LDLHSGYHQI PMEPKDRYKT AFVTPSGKYE YTVMPFGLVN 750
    APSTFARYMA DTFRDLRFVN VYLDDILIFS ESPEEHWKHL DTVLERLKNE 800
    NLIVKKKKCK FASEETEFLG YSIGIQKIAP LQHKCAAIRD FPTPKTVKQA 850
    QRFLGMINYY RRFIPNCSKI AQPIQLFICD KSQWTEKQDK AIEKLKAALC 900
    NSPVLVPFNN KANYRLTTDA SKDGIGAVLE EVDNKNKLVG VVGYFSKSLE 950
    SAQKNYPAGE LELLGIIKAL HHFRYMLHGK HFTLRTDHIS LLSLQNKNEP 1000
    ARRVQRWLDD LATYDFTLEY LAGPKNVVAD AISRAIYTIT PETSRPIDTE 1050
    SWKSYYKSDP LCSAVLIHMK ELTQHNVTPE DMSAFRSYQK KLELSETFRK 1100
    NYSLEDEMIY YQDRLVVPIK QQNAVMRLYH DHTLFGGHFG VTVTLAKISP 1150
    IYYWPKLQHS IIQYIRTCVQ CQLIKSHRPR LHGLLQPLPI AEGRWLDISM 1200
    DFVTGLPPTS NNLNMILVVV DRFSKRAHFI ATRKTLDATQ LIDLLFRYIF 1250
    SYHGFPRTIT SDRDVRMTAD KYQELTKRLG IKSTMSSANH PQTDGQSERT 1300
    IQTLNRLLRA YVSTNIQNWH VYLPQIEFVY NSTPTRTLGK SPFEIDLGYL 1350
    PNTPAIKSDD EVNARSFTAV ELAKHLKALT IQTKEQLEHA QIEMETNNNQ 1400
    RRKPLLLNIG DHVLVHRDAY FKKGAYMKVQ QIYVGPFRVV KKINDNAYEL 1450
    DLNSHKKKHR VINVQFLKSL YTVQTRTQRI NQSAPLRELR EHTKLLHS 1498

    Note: Produced by +1 ribosomal frameshifting between codon Ala-285 and Val-286 of the YIL082W ORF.

    Length:1,498
    Mass (Da):172,369
    Last modified:March 6, 2007 - v2
    Checksum:i4E51C3EFBDEFD7E4
    GO
    Isoform Transposon Ty3-I Gag polyprotein (identifier: Q99219-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry Q99219.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:290
    Mass (Da):34,100
    GO

    Sequence cautioni

    The sequence AAA35184.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence CAA86713.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence DAA08470.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti502 – 5021G → A in AAA35184. (PubMed:2854194)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M23367 Genomic DNA. Translation: AAA35184.1. Sequence problems.
    Z46728 Genomic DNA. Translation: CAA86713.1. Sequence problems.
    Z37997 Genomic DNA. Translation: CAA86090.1.
    BK006942 Genomic DNA. Translation: DAA08470.1. Sequence problems.
    PIRiS53577.
    RefSeqiNP_012184.1. NM_001181434.3.

    Genome annotation databases

    GeneIDi854728.
    KEGGisce:YIL082W-A.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M23367 Genomic DNA. Translation: AAA35184.1 . Sequence problems.
    Z46728 Genomic DNA. Translation: CAA86713.1 . Sequence problems.
    Z37997 Genomic DNA. Translation: CAA86090.1 .
    BK006942 Genomic DNA. Translation: DAA08470.1 . Sequence problems.
    PIRi S53577.
    RefSeqi NP_012184.1. NM_001181434.3.

    3D structure databases

    ProteinModelPortali Q7LHG5.
    SMRi Q7LHG5. Positions 576-1037, 1137-1359.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34910. 5 interactions.
    IntActi Q7LHG5. 3 interactions.
    MINTi MINT-541560.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 854728.
    KEGGi sce:YIL082W-A.

    Organism-specific databases

    SGDi S000003537. YIL082W-A.

    Phylogenomic databases

    HOGENOMi HOG000172599.
    KOi K07497.
    OrthoDBi EOG7HF1TD.

    Miscellaneous databases

    NextBioi 977418.

    Gene expression databases

    Genevestigatori Q7LHG5.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    InterProi IPR001584. Integrase_cat-core.
    IPR024650. Peptidase_A2B.
    IPR021109. Peptidase_aspartic_dom.
    IPR005162. Retrotrans_gag_dom.
    IPR012337. RNaseH-like_dom.
    IPR000477. RT_dom.
    IPR001878. Znf_CCHC.
    [Graphical view ]
    Pfami PF12384. Peptidase_A2B. 1 hit.
    PF03732. Retrotrans_gag. 1 hit.
    PF00665. rve. 1 hit.
    PF00078. RVT_1. 1 hit.
    [Graphical view ]
    SMARTi SM00343. ZnF_C2HC. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50630. SSF50630. 1 hit.
    SSF53098. SSF53098. 1 hit.
    SSF57756. SSF57756. 1 hit.
    PROSITEi PS50994. INTEGRASE. 1 hit.
    PS50878. RT_POL. 1 hit.
    PS50158. ZF_CCHC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses."
      Hansen L.J., Chalker D.L., Sandmeyer S.B.
      Mol. Cell. Biol. 8:5245-5256(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein."
      Hansen L.J., Sandmeyer S.B.
      J. Virol. 64:2599-2607(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    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 nameiYI31B_YEAST
    AccessioniPrimary (citable) accession number: Q7LHG5
    Secondary accession number(s): D6VVK4
    , Q04717, Q04722, Q05350
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 6, 2007
    Last sequence update: March 6, 2007
    Last modified: October 1, 2014
    This is version 94 of the entry and version 2 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. Ty3 retrotransposons belong to the gypsy-like elements (metaviridae).
    In contrast to Ty3-1 (Ty3-G), Ty3-2 (Ty3-I) is a transpositionally inactive element. The Ty3-2 ORF is truncated by the deletion of a single nucleotide, which causes a frameshift mutation when compared with Ty3-1.

    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 IX
      Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

    External Data

    Dasty 3