P0CX75 (YL13A_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transposon Ty1-LR3 Gag polyprotein

Alternative name(s):
Gag-p49
Transposon Ty1 protein A
Short name=TY1A
Short name=TYA
p58

Cleaved into the following 2 chains:

1. Capsid protein
   Short name=CA
   Alternative name(s):
   Gag-p45
   p54
2. Gag-p4

Gene names

Name:	TY1A-LR3
Synonyms:	YLRWTy1-3 GAG
Ordered Locus Names:	YLR227W-A
ORF Names:	L8083.11

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	440 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subunit structure	Homotrimer By similarity.
Subcellular location	Cytoplasm By similarity.
Induction	Ty1-LR3 is a highly expressed element. Induced under amino acid starvation conditions by GCN4. Ref.5
Domain	The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities By similarity.
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).

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Ribosomal frameshifting
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome Transposable element
Gene Ontology (GO)
Biological_process	transposition, RNA-mediated Inferred from sequence or structural similarity Ref.4. Source: SGD
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell retrotransposon nucleocapsid Inferred from sequence or structural similarity Ref.4. Source: SGD
Molecular_function	RNA binding Inferred from sequence or structural similarity Ref.4. Source: SGD
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

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).

Isoform Transposon Ty1-LR3 Gag polyprotein (identifier: P0CX75-1)

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.

Note: Produced by conventional translation.

Isoform Transposon Ty1-LR3 Gag-Pol polyprotein (identifier: P0C2I6-1)

The sequence of this isoform can be found in the external entry P0C2I6.
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 YLR227W-A ORF.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 440	440	Transposon Ty1-LR3 Gag polyprotein		PRO_0000409800
	Chain	1 – 401	401	Capsid protein By similarity		PRO_0000409801
	Peptide	402 – 440	39	Gag-p4 By similarity		PRO_0000409802
Regions
	Region	299 – 401	103	RNA-binding By similarity
	Compositional bias	64 – 146	83	Pro-rich
Sites
	Site	401 – 402	2	Cleavage; by Ty1 protease By similarity
Amino acid modifications
	Modified residue	439	1	Phosphothreonine Ref.7
Experimental info
	Sequence conflict	255	1	S → G in AAU09762. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty1-LR3 Gag polyprotein [UniParc]. Last modified June 28, 2011. Version 1. Checksum: ACC50DD2AC8F4781	FASTA	440	48,993
	10 20 30 40 50 60 MESQQLSQHS HISHGSACAS VTSKEVHTNQ DPLDVSASKT EECEKASTKA NSQQTTTPAS 70 80 90 100 110 120 SAVPENPHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG WSFYGHPSMI PYTPYQMSPM 130 140 150 160 170 180 YFPPGPQSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND 190 200 210 220 230 240 FPNWVKTYIK FLQNSNLGGI IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI 250 260 270 280 290 300 LSVDYTDIMK ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN 310 320 330 340 350 360 GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ QGSRNSKPNY 370 380 390 400 410 420 RRNLSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA HNVSTSNNSP STDNDSISKS 430 440 TTEPIQLNNK HDLHLRPGTY
	Isoform Transposon Ty1-LR3 Gag-Pol polyprotein [UniParc]. See P0C2I6.		–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"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.
[5]	"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.
[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.
[7]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-439, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U19027 Genomic DNA. No translation available. AY723845 Genomic DNA. Translation: AAU09762.1. BK006945 Genomic DNA. Translation: DAA09545.1.
PIR	S57044.
RefSeq	NP_012561.3. NM_001181684.3. NP_013673.1. NM_001182398.1. NP_058172.1. NM_001184407.1.
3D structure databases
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YJR026W; YJR026W; YJR026W. YLR227W-A; YLR227W-A; YLR227W-A. YML040W; YML040W; YML040W.
GeneID	850926. 853483. 854968.
KEGG	sce:YJR026W. sce:YLR227W-A. sce:YML040W.
Organism-specific databases
CYGD	YLR227w-a.
SGD	S000007375. YLR227W-A.
Gene expression databases
ArrayExpress	P0CX75.
GermOnline	YLR227W-A. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR015820. Retrotransposon_Ty1A_N. [Graphical view]
Pfam	PF01021. TYA. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	967358.

Entry information

Entry name

YL13A_YEAST

Accession

Primary (citable) accession number: P0CX75
Secondary accession number(s): D6VWK0, P47097, Q66R50

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 28, 2011
Last sequence update:	June 28, 2011
Last modified:	May 29, 2013
This is version 14 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program