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Protein

Transposon Ty1-BL Gag polyprotein

Gene

TY1A-BL

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei401 – 4022Cleavage; by Ty1 proteaseBy similarity

GO - Molecular functioni

  • RNA binding Source: SGD

GO - Biological processi

  • transposition, RNA-mediated Source: SGD
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Transposon Ty1-BL Gag polyprotein
Alternative name(s):
Gag-p49
Transposon Ty1 protein A
Short name:
TY1A
Short name:
TYA
p58
Cleaved into the following 2 chains:
Capsid protein
Short name:
CA
Alternative name(s):
Gag-p45
p54
Gene namesi
Name:TY1A-BL
Synonyms:YBLWTy1-1 GAG
Ordered Locus Names:YBL005W-A
ORF Names:YBL004W-B, YBL0324
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome II

Organism-specific databases

CYGDiYBL005w-a.
SGDiS000002146. YBL005W-A.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 440440Transposon Ty1-BL Gag polyproteinPRO_0000278990Add
BLAST
Chaini1 – 401401Capsid proteinBy similarityPRO_0000278991Add
BLAST
Peptidei402 – 44039Gag-p4By similarityPRO_0000278992Add
BLAST

Proteomic databases

PaxDbiQ12266.

Expressioni

Inductioni

Ty1-BL is a highly expressed element. Induced under amino acid starvation conditions by GCN4.1 Publication

Interactioni

Subunit structurei

Homotrimer.By similarity

Protein-protein interaction databases

BioGridi32695. 5 interactions.
IntActiQ12266. 2 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ12266.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni299 – 401103RNA-bindingBy similarityAdd
BLAST

Domaini

The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities.By similarity

Phylogenomic databases

eggNOGiNOG12793.
GeneTreeiENSGT00710000106943.
HOGENOMiHOG000000740.
InParanoidiQ12266.
OrthoDBiEOG7TJ3S3.

Family and domain databases

InterProiIPR015820. Retrotransposon_Ty1A_N.
[Graphical view]
PfamiPF01021. TYA. 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. AlignAdd to basket

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-BL Gag polyprotein (identifier: Q12266-1) [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

        10         20         30         40         50
MESQQLSQHS PIFHGSACAS VTSKEVQTTQ DPLDISASKT EECEKVSTQA
60 70 80 90 100
NSQQPTTPPS SAVPENHHHA SPQAAQVPLP QNGPYPQQRM MNTQQANISG
110 120 130 140 150
WPVYGHPSLM PYPPYQMSPM YAPPGAQSQF TQYPQYVGTH LNTPSPESGN
160 170 180 190 200
SFPDSSSAKS NMTSTNQHVR PPPILTSPND FLNWVKIYIK FLQNSNLGDI
210 220 230 240 250
IPTATRKAVR QMTDDELTFL CHTFQLFAPS QFLPPWVKDI LSVDYTDIMK
260 270 280 290 300
ILSKSINKMQ SDTQEVNDIT TLATLHYNGS TPADAFEAEV TNILDRLNNN
310 320 330 340 350
GIPINNKVAC QFIMRGLSGE YKFLPYARHR CIHMTVADLF SDIHSMYEEQ
360 370 380 390 400
QESKRNKSTY RRSPSDEKKD SRTYTNTTKP KSITRNSQKP NNSQSRTARA
410 420 430 440
HNVSTFNNSP GPDNDLIRGS TTEPIQLKNT HDLHLRPGTY
Note: Produced by conventional translation.
Length:440
Mass (Da):49,285
Last modified:November 1, 1996 - v1
Checksum:iEBE246012C88C029
GO
Isoform Transposon Ty1-BL Gag-Pol polyprotein (identifier: Q12490-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry Q12490.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YBL005W-A ORF.
Length:1,755
Mass (Da):198,969
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z35765 Genomic DNA. Translation: CAA84819.1.
Z35766 Genomic DNA. Translation: CAA84823.1.
BK006936 Genomic DNA. Translation: DAA07117.1.
PIRiS45737.
RefSeqiNP_009550.1. NM_001180047.1. [Q12266-1]

Genome annotation databases

EnsemblFungiiYBL005W-A; YBL005W-A; YBL005W-A. [Q12266-1]
GeneIDi852279.
KEGGisce:YBL005W-A.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z35765 Genomic DNA. Translation: CAA84819.1.
Z35766 Genomic DNA. Translation: CAA84823.1.
BK006936 Genomic DNA. Translation: DAA07117.1.
PIRiS45737.
RefSeqiNP_009550.1. NM_001180047.1. [Q12266-1]

3D structure databases

ProteinModelPortaliQ12266.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32695. 5 interactions.
IntActiQ12266. 2 interactions.

Proteomic databases

PaxDbiQ12266.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBL005W-A; YBL005W-A; YBL005W-A. [Q12266-1]
GeneIDi852279.
KEGGisce:YBL005W-A.

Organism-specific databases

CYGDiYBL005w-a.
SGDiS000002146. YBL005W-A.

Phylogenomic databases

eggNOGiNOG12793.
GeneTreeiENSGT00710000106943.
HOGENOMiHOG000000740.
InParanoidiQ12266.
OrthoDBiEOG7TJ3S3.

Miscellaneous databases

NextBioi970902.

Family and domain databases

InterProiIPR015820. Retrotransposon_Ty1A_N.
[Graphical view]
PfamiPF01021. TYA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete DNA sequence of yeast chromosome II."
    Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
    , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
    EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
    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. "Differential effects of chromatin and Gcn4 on the 50-fold range of expression among individual yeast Ty1 retrotransposons."
    Morillon A., Benard L., Springer M., Lesage P.
    Mol. Cell. Biol. 22:2078-2088(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  5. "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.
  6. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  7. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiYB11A_YEAST
AccessioniPrimary (citable) accession number: Q12266
Secondary accession number(s): D6VPZ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: November 1, 1996
Last modified: July 22, 2015
This is version 87 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, Reference proteome, Transposable element

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.