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Q04215

- YM13A_YEAST

UniProt

Q04215 - YM13A_YEAST

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Protein

Transposon Ty1-MR1 Gag polyprotein

Gene

TY1A-MR1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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

  1. RNA binding Source: SGD

GO - Biological processi

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

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Transposon Ty1-MR1 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-MR1
Synonyms:YMRCTy1-3 GAG
Ordered Locus Names:YMR046C
ORF Names:YM9532.11C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIII

Organism-specific databases

CYGDiYMR046c.
SGDiS000004649. YMR046C.

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 440440Transposon Ty1-MR1 Gag polyproteinPRO_0000203499Add
BLAST
Chaini1 – 401401Capsid proteinBy similarityPRO_0000279131Add
BLAST
Peptidei402 – 44039Gag-p4By similarityPRO_0000279132Add
BLAST

Proteomic databases

MaxQBiQ04215.

Expressioni

Inductioni

Ty1-MR1 is a weakly expressed element. Induced under amino acid starvation conditions by GCN4.1 Publication

Gene expression databases

GenevestigatoriQ04215.

Interactioni

Subunit structurei

Homotrimer.By similarity

Protein-protein interaction databases

BioGridi35219. 9 interactions.
IntActiQ04215. 2 interactions.
STRINGi4932.YMR046C.

Structurei

3D structure databases

ProteinModelPortaliQ04215.
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

GeneTreeiENSGT00710000106943.
HOGENOMiHOG000000740.
InParanoidiQ04215.
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. 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-MR1 Gag polyprotein (identifier: Q04215-1) [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 PISHGSACAS VTSKEVQTTQ DPLDISASKT EECEKVSTQA
60 70 80 90 100
NSQQPTTPLS 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 YKFLRYARHR CIHMTVADLF SDIHSMYEEQ
360 370 380 390 400
QESKRNKSTH RRSPSDEKKD SRTYTNTTKP KSITRNSQKP NNSQSRTARA
410 420 430 440
HNVSTFNNSP GPDNDLIRGS TTEPIQLKNT HDLHLRPGTY

Note: Produced by conventional translation.

Length:440
Mass (Da):49,274
Last modified:November 1, 1997 - v1
Checksum:i6948648D0FEE321E
GO
Isoform Transposon Ty1-MR1 Gag-Pol polyprotein (identifier: Q04214-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q04214.
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 YMR046C ORF.

Length:1,755
Mass (Da):198,899
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48502 Genomic DNA. Translation: CAA88412.1.
BK006946 Genomic DNA. Translation: DAA09945.1.
PIRiS52895.
RefSeqiNP_013760.1. NM_001182543.1. [Q04215-1]

Genome annotation databases

EnsemblFungiiYMR046C; YMR046C; YMR046C. [Q04215-1]
GeneIDi855063.
KEGGisce:YMR046C.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48502 Genomic DNA. Translation: CAA88412.1 .
BK006946 Genomic DNA. Translation: DAA09945.1 .
PIRi S52895.
RefSeqi NP_013760.1. NM_001182543.1. [Q04215-1 ]

3D structure databases

ProteinModelPortali Q04215.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35219. 9 interactions.
IntActi Q04215. 2 interactions.
STRINGi 4932.YMR046C.

Proteomic databases

MaxQBi Q04215.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YMR046C ; YMR046C ; YMR046C . [Q04215-1 ]
GeneIDi 855063.
KEGGi sce:YMR046C.

Organism-specific databases

CYGDi YMR046c.
SGDi S000004649. YMR046C.

Phylogenomic databases

GeneTreei ENSGT00710000106943.
HOGENOMi HOG000000740.
InParanoidi Q04215.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 978324.

Gene expression databases

Genevestigatori Q04215.

Family and domain databases

InterProi IPR015820. Retrotransposon_Ty1A_N.
[Graphical view ]
Pfami PF01021. TYA. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. "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 nameiYM13A_YEAST
AccessioniPrimary (citable) accession number: Q04215
Secondary accession number(s): D6VZM1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 26, 2014
This is version 86 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 XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3