Q12173 (YG31A_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transposon Ty3-G Gag polyprotein

Alternative name(s):
Gag3
Transposon Ty3-1 protein A
Short name=TY3A

Cleaved into the following 3 chains:

1. Capsid protein
   Short name=CA
   Alternative name(s):
   p24
2. Spacer peptide p3
3. Nucleocapsid protein p9
   Short name=NC
   Short name=NCp9
   Alternative name(s):
   p7

Gene names

Name:	TY3A-G
Synonyms:	YGRWTy3-1 GAG
Ordered Locus Names:	YGR109W-A
ORF Names:	G5982

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	290 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. Ref.1 Ref.9 Ref.10 Ref.12 Nucleocapsid protein p9 (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. Ref.1 Ref.9 Ref.10 Ref.12
Subcellular location	Cytoplasm Ref.7.
Domain	The N-terminal domain of NC, but not its zinc finger, is required for nucleoprotein complex formation and its chaperone activities.
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).
Sequence similarities	Contains 1 CCHC-type zinc finger.
Sequence caution	The sequence AAA98434.2 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Ribosomal frameshifting
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Technical term	Complete proteome Reference proteome Transposable element
Gene Ontology (GO)
Biological_process	transposition, RNA-mediated Inferred from mutant phenotype PubMed 17442718. Source: SGD
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell retrotransposon nucleocapsid Inferred from direct assay Ref.14. Source: SGD
Molecular_function	DNA binding Inferred from direct assay PubMed 21917850. Source: SGD zinc ion binding Inferred from electronic annotation. Source: InterPro
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.

Isoform Transposon Ty3-G Gag polyprotein (identifier: Q12173-1)

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 Ty3-G Gag-Pol polyprotein (identifier: Q99315-1)

The sequence of this isoform can be found in the external entry Q99315.
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 Ala-285 and Val-286 of the YGR109W-A ORF.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Ref.14
	Chain	2 – 290	289	Transposon Ty3-G Gag polyprotein		PRO_5000143279
	Chain	2 – 207	206	Capsid protein		PRO_0000279365
	Peptide	208 – 233	26	Spacer peptide p3		PRO_0000279366
	Chain	234 – 290	57	Nucleocapsid protein p9		PRO_5000143280
Regions
	Zinc finger	265 – 282	18	CCHC-type
Sites
	Site	207 – 208	2	Cleavage; by Ty3 protease
	Site	233 – 234	2	Cleavage; by Ty3 protease
Experimental info
	Mutagenesis	267	1	C → S: Reduces level of VLP formation and maturation. Ref.9
	Mutagenesis	275	1	H → Q: Reduces level of VLP formation and maturation. Ref.9

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty3-G Gag polyprotein [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 4D63E26BDE78197F	FASTA	290	34,027
	10 20 30 40 50 60 MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND 70 80 90 100 110 120 ASRIVYCRRH LLNPAAQWAN DFVQEQGILE ITFDTFIQGL YQHFYKPPDI NKIFNAITQL 130 140 150 160 170 180 SEAKLGIERL NQRFRKIWDR MPPDFMTEKA AIMTYTRLLT KETYNIVRMH KPETLKDAME 190 200 210 220 230 240 EAYQTTALTE RFFPGFELDA DGDTIIGATT HLQEEYDSDY DSEDNLTQNG YVHTVRTRRS 250 260 270 280 290 YNKPMSNHRN RRNNNPSREE CIKNRLCFYC KKEGHRLNEC RARKASSNRS
	Isoform Transposon Ty3-G Gag-Pol polyprotein [UniParc]. See Q99315.		–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION. Strain: AB950.
[2]	"The sequence of a 23.4 kb segment on the right arm of chromosome VII from Saccharomyces cerevisiae reveals CLB6, SPT6, RP28A and NUP57 genes, a Ty3 element and 11 new open reading frames." Hansen M., Albers M., Backes U., Coblenz A., Leuther H., Neu R., Schreer A., Schaefer B., Zimmermann M., Wolf K. Yeast 12:1273-1277(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"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.
[6]	"A yeast sigma composite element, TY3, has properties of a retrotransposon." Clark D.J., Bilanchone V.W., Haywood L.J., Dildine S.L., Sandmeyer S.B. J. Biol. Chem. 263:1413-1423(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
[7]	"Ty3 GAG3 and POL3 genes encode the components of intracellular particles." Hansen L.J., Chalker D.L., Orlinsky K.J., Sandmeyer S.B. J. Virol. 66:1414-1424(1992) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[8]	"Proteolytic processing of Ty3 proteins is required for transposition." Kirchner J., Sandmeyer S.B. J. Virol. 67:19-28(1993) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEOLYTIC PROCESSING, CLEAVAGE SITES.
[9]	"The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins." Orlinsky K.J., Sandmeyer S.B. J. Virol. 68:4152-4166(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF NUCLEOCAPSID, MUTAGENESIS OF CYS-267 AND HIS-275.
[10]	"The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7." Gabus C., Ficheux D., Rau M., Keith G., Sandmeyer S.B., Darlix J.-L. EMBO J. 17:4873-4880(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"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.
[12]	"Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro." Cristofari G., Gabus C., Ficheux D., Bona M., Le Grice S.F.J., Darlix J.-L. J. Biol. Chem. 274:36643-36648(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"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.
[14]	"Investigation by atomic force microscopy of the structure of Ty3 retrotransposon particles." Kuznetsov Y.G., Zhang M., Menees T.M., McPherson A., Sandmeyer S.B. J. Virol. 79:8032-8045(2005) [PubMed] [Europe PMC] [Abstract] Cited for: CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, CLEAVAGE SITE GLY-207-208-ALA, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M34549 Genomic DNA. Translation: AAA98434.2. Different initiation. Z72894 Genomic DNA. Translation: CAA97114.1. Z72895 Genomic DNA. Translation: CAA97116.1. AY557824 Genomic DNA. Translation: AAS56150.1. M18353 Genomic DNA. Translation: AAA66936.1. BK006941 Genomic DNA. Translation: DAA08203.1.
PIR	S22875. S69841.
RefSeq	NP_058162.3. NM_001184380.3.
3D structure databases
ProteinModelPortal	Q12173.
ModBase	Search...
Protein-protein interaction databases
STRING	4932.YGR109W-A.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YGR109W-A; YGR109W-A; YGR109W-A.
GeneID	853005.
KEGG	sce:YGR109W-A. sce:YGR117C.
Organism-specific databases
CYGD	YGR109w-a.
SGD	S000007346. YGR109W-A.
Phylogenomic databases
GeneTree	ENSGT00700000104358.
HOGENOM	HOG000155559.
Gene expression databases
Genevestigator	Q12173.
Family and domain databases
InterPro	IPR005162. Retrotrans_gag. IPR001878. Znf_CCHC. [Graphical view]
Pfam	PF03732. Retrotrans_gag. 1 hit. [Graphical view]
SMART	SM00343. ZnF_C2HC. 1 hit. [Graphical view]
PROSITE	PS50158. ZF_CCHC. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	972854.

Entry information

Entry name

YG31A_YEAST

Accession

Primary (citable) accession number: Q12173
Secondary accession number(s): D6VUP2, Q07096, Q9P311

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program