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P0CX63

- YF21B_YEAST

UniProt

P0CX63 - YF21B_YEAST

Protein

Transposon Ty2-F Gag-Pol polyprotein

Gene

TY2B-F

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 26 (01 Oct 2014)
      Sequence version 1 (28 Jun 2011)
      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 Ty2 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
    Sitei397 – 3982Cleavage; by Ty2 proteaseBy similarity
    Active sitei457 – 4571For protease activity; shared with dimeric partnerBy similarity
    Sitei578 – 5792Cleavage; by Ty2 proteaseBy similarity
    Metal bindingi667 – 6671Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Metal bindingi732 – 7321Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
    Sitei1232 – 12332Cleavage; by Ty2 proteaseBy similarity
    Metal bindingi1361 – 13611Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1442 – 14421Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1443 – 14431Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
    Metal bindingi1625 – 16251Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1667 – 16671Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
    Metal bindingi1700 – 17001Magnesium; 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

    Enzyme and pathway databases

    BRENDAi2.7.7.49. 250.
    2.7.7.7. 250.
    3.1.26.4. 250.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Transposon Ty2-F Gag-Pol polyprotein
    Alternative name(s):
    TY2A-TY2B
    Transposon Ty2 TYA-TYB polyprotein
    Cleaved into the following 4 chains:
    Capsid protein
    Short name:
    CA
    Ty2 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:TY2B-F
    Synonyms:YFLWTy2-1 POL
    Ordered Locus Names:YFL002W-A
    ORF Names:FN01
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VI

    Organism-specific databases

    CYGDiYFL002w-a.
    SGDiS000002962. YFL002W-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 – 17701770Transposon Ty2-F Gag-Pol polyproteinPRO_0000279308Add
    BLAST
    Chaini1 – 397397Capsid proteinBy similarityPRO_0000279309Add
    BLAST
    Chaini398 – 578181Ty2 proteaseBy similarityPRO_0000279310Add
    BLAST
    Chaini579 – 1232654IntegraseBy similarityPRO_0000279311Add
    BLAST
    Chaini1233 – 1770538Reverse transcriptase/ribonuclease HBy similarityPRO_0000279312Add
    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

    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

    BioGridi31146. 4 interactions.
    33410. 4 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliP0CX63.
    SMRiP0CX63. Positions 632-833.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini656 – 831176Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST
    Domaini1353 – 1491139Reverse transcriptase Ty1/copia-typeAdd
    BLAST
    Domaini1625 – 1767143RNase H Ty1/copia-typeAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni295 – 397103RNA-bindingBy similarityAdd
    BLAST
    Regioni579 – 63658Integrase-type zinc finger-likeAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1193 – 122735Bipartite nuclear localization signalBy similarityAdd
    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

    HOGENOMiHOG000280731.
    OrthoDBiEOG7TJ3S3.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    InterProiIPR025724. GAG-pre-integrase_dom.
    IPR001584. Integrase_cat-core.
    IPR015820. Retrotransposon_Ty1A_N.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    [Graphical view]
    PfamiPF13976. gag_pre-integrs. 1 hit.
    PF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    PF01021. TYA. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    PROSITEiPS50994. 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.

    Isoform Transposon Ty2-F Gag-Pol polyprotein (identifier: P0CX63-1) [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

    MESQQLHQNP HSLHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV     50
    NSQQETTPGT SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN 100
    WAHYQQPSMM TCSHYQTSPA YYQPDPHYPL PQYIPPLSTS SPDPIDSQNQ 150
    HSEVPQAETK VRNNVLPPHT LTSEENFSTW VKFYIRFLKN SNLGDIIPND 200
    QGEIKSQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN YADILTVLCK 250
    SVSKMQTNNQ ELKDWIALAN LEYDGSTSAD TFEITVSTII QRLKENNINV 300
    SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN 350
    LNKPSQYKQH SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA 400
    TSSKFSRVNN DHINESTVSS QYLSDDNELS LGQQQKESKP THTIDSNDEL 450
    PDHLLIDSGA SQTLVRSAHY LHHATPNSEI NIVDAQKQDI PINAIGNLHF 500
    NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN TLERSDGTVL 550
    APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH 600
    ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS 650
    RLKYQESYEP FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH 700
    DRREESILNV FTSILAFIKN QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG 750
    ITACYTTTAD SRAHGVAERL NRTLLNDCRT LLHCSGLPNH LWFSAVEFST 800
    IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN HNPDSKIHPR 850
    GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQDKQS KLDQFNYDTL 900
    TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND 950
    FSSQSINPLQ LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE 1000
    STEMGGTVES DTTSPRHSST FTARNQNRPG STNEMIDLTS QDRVNYGLEN 1050
    IKTTRLGGTE EPYIQRNSDT NIKYRTTNST PSIDDRSSNS ESTTPIISIE 1100
    TKAVCDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD SILDDLPLPD 1150
    LTHKSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN 1200
    ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD 1250
    EAITYNKDNK EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN 1300
    SMFIFNKKRD GTHKARFVAR GDIQHPDTYD SDMQSNTVHH YALMTSLSIA 1350
    LDNDYYITQL DISSAYLYAD IKEELYIRPP PHLGLNDKLL RLRKSLYGLK 1400
    QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF VDDMILFSKD 1450
    LNANKKIITT LKKQYDTKII NLGESDNEIQ YDILGLEIKY QRSKYMKLGM 1500
    EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE 1550
    MQKLIGLASY VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD 1600
    TRDKQLIWHK NKPTKPDNKL VAISDASYGN QPYYKSQIGN IFLLNGKVIG 1650
    GKSTKASLTC TSTTEAEIHA VSEAIPLLNN LSHLVQELNK KPIIKGLLTD 1700
    SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY YIETKKNIAD 1750
    VMTKPLPIKT FKLLTNKWIH 1770

    Note: Produced by +1 ribosomal frameshifting between codon Leu-431 and Gly-432 of the YFL002W-B ORF.

    Length:1,770
    Mass (Da):202,039
    Last modified:June 28, 2011 - v1
    Checksum:i97C0C8F7D431D731
    GO
    Isoform Transposon Ty2-F Gag polyprotein (identifier: P0CX61-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry P0CX61.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:438
    Mass (Da):49,762
    GO

    Sequence cautioni

    The sequence BAA09237.1 differs from that shown. Reason: Erroneous gene model prediction.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D50617 Genomic DNA. Translation: BAA09237.1. Sequence problems.
    BK006940 Genomic DNA. Translation: DAA12437.1.
    PIRiS58651.
    RefSeqiNP_058163.1. NM_001184402.1. [P0CX63-1]
    NP_116653.1. NM_001180862.1. [P0CX63-1]

    Genome annotation databases

    EnsemblFungiiYFL002W-A; YFL002W-A; YFL002W-A. [P0CX63-1]
    YGR161W-B; YGR161W-B; YGR161W-B. [P0CX63-1]
    GeneIDi850548.
    853067.
    KEGGisce:YFL002W-A.
    sce:YGR161W-B.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D50617 Genomic DNA. Translation: BAA09237.1 . Sequence problems.
    BK006940 Genomic DNA. Translation: DAA12437.1 .
    PIRi S58651.
    RefSeqi NP_058163.1. NM_001184402.1. [P0CX63-1 ]
    NP_116653.1. NM_001180862.1. [P0CX63-1 ]

    3D structure databases

    ProteinModelPortali P0CX63.
    SMRi P0CX63. Positions 632-833.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31146. 4 interactions.
    33410. 4 interactions.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YFL002W-A ; YFL002W-A ; YFL002W-A . [P0CX63-1 ]
    YGR161W-B ; YGR161W-B ; YGR161W-B . [P0CX63-1 ]
    GeneIDi 850548.
    853067.
    KEGGi sce:YFL002W-A.
    sce:YGR161W-B.

    Organism-specific databases

    CYGDi YFL002w-a.
    SGDi S000002962. YFL002W-A.

    Phylogenomic databases

    HOGENOMi HOG000280731.
    OrthoDBi EOG7TJ3S3.

    Enzyme and pathway databases

    BRENDAi 2.7.7.49. 250.
    2.7.7.7. 250.
    3.1.26.4. 250.

    Miscellaneous databases

    NextBioi 966321.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    InterProi IPR025724. GAG-pre-integrase_dom.
    IPR001584. Integrase_cat-core.
    IPR015820. Retrotransposon_Ty1A_N.
    IPR012337. RNaseH-like_dom.
    IPR013103. RVT_2.
    [Graphical view ]
    Pfami PF13976. gag_pre-integrs. 1 hit.
    PF00665. rve. 1 hit.
    PF07727. RVT_2. 1 hit.
    PF01021. TYA. 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 nameiYF21B_YEAST
    AccessioniPrimary (citable) accession number: P0CX63
    Secondary accession number(s): D6VTM7, Q05369, Q12503
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 28, 2011
    Last sequence update: June 28, 2011
    Last modified: October 1, 2014
    This is version 26 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. Ty2 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 VI
      Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

    External Data

    Dasty 3