Q03612 (YE11B_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transposon Ty1-ER1 Gag-Pol polyprotein

Alternative name(s):
Gag-Pol-p199
TY1A-TY1B
Transposon Ty1 TYA-TYB polyprotein
p190

Cleaved into the following 4 chains:

1. Capsid protein
   Short name=CA
   Alternative name(s):
   Gag-p45
   p54
2. Ty1 protease
   Short name=PR
   EC=3.4.23.-
   Alternative name(s):
   Pol-p20
   p23
3. Integrase
   Short name=IN
   Alternative name(s):
   Pol-p71
   p84
   p90
4. Reverse transcriptase/ribonuclease H
   Short name=RT
   EC=2.7.7.49
   EC=2.7.7.7
   EC=3.1.26.4
   Alternative name(s):
   Pol-p63
   p60

Gene names

Name:	TY1B-ER1
Synonyms:	YERCTy1-1 POL
Ordered Locus Names:	YER138C

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	1755 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. 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. 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.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Endonucleolytic cleavage to 5'-phosphomonoester.
Subunit structure	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.
Subcellular location	Cytoplasm. Nucleus By similarity.
Domain	The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities By similarity. Ref.5 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,D35E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity. Ref.5
Post-translational modification	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 yielding capsid protein p45 and a Pol-p154 precursor protein. This cleavage is a prerequisite for subsequent processing of Pol-p154 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.
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).
Sequence similarities	Contains 1 integrase catalytic domain. Contains 1 peptidase A11 domain. Contains 1 reverse transcriptase Ty1/copia-type domain. Contains 1 RNase H Ty1/copia-type domain.

Ontologies

Keywords
Biological process	Capsid maturation DNA integration DNA recombination Transposition
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Ribosomal frameshifting
Domain	Zinc-finger
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding RNA-binding Zinc
Molecular function	Aspartyl protease DNA-directed DNA polymerase Endonuclease Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed DNA polymerase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Multifunctional enzyme Reference proteome Transposable element
Gene Ontology (GO)
Biological_process	DNA integration Inferred from electronic annotation. Source: UniProtKB-KW DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transposition, RNA-mediated Inferred from sequence or structural similarity Ref.3. Source: SGD viral procapsid maturation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell retrotransposon nucleocapsid Inferred from sequence or structural similarity Ref.3. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from sequence or structural similarity Ref.3. Source: SGD RNA binding Inferred from sequence or structural similarity Ref.3. Source: SGD RNA-directed DNA polymerase activity Inferred from sequence or structural similarity Ref.3. Source: SGD aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW peptidase activity Inferred from sequence or structural similarity Ref.3. Source: SGD ribonuclease H activity Inferred from electronic annotation. Source: EC ribonuclease activity Inferred from sequence or structural similarity Ref.3. 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-ER1 Gag-Pol polyprotein (identifier: Q03612-1)

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 +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YER137C-A ORF.

Isoform Transposon Ty1-ER1 Gag polyprotein (identifier: P0CX71-1)

The sequence of this isoform can be found in the external entry P0CX71.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1755	1755	Transposon Ty1-ER1 Gag-Pol polyprotein		PRO_0000279043
	Chain	1 – 401	401	Capsid protein By similarity		PRO_0000279044
	Chain	402 – 582	181	Ty1 protease By similarity		PRO_0000279045
	Chain	583 – 1217	635	Integrase By similarity		PRO_0000279046
	Chain	1218 – 1755	538	Reverse transcriptase/ribonuclease H By similarity		PRO_0000279047
Regions
	Domain	660 – 835	176	Integrase catalytic
	Domain	1338 – 1476	139	Reverse transcriptase Ty1/copia-type
	Domain	1610 – 1752	143	RNase H Ty1/copia-type
	Region	299 – 401	103	RNA-binding By similarity
	Region	583 – 640	58	Integrase-type zinc finger-like
	Motif	1178 – 1212	35	Bipartite nuclear localization signal By similarity
	Compositional bias	64 – 146	83	Pro-rich
Sites
	Active site	461	1	For protease activity; shared with dimeric partner By similarity
	Metal binding	671	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	736	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	1346	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1427	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1428	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1610	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1652	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1685	1	Magnesium; catalytic; for RNase H activity By similarity
	Site	401 – 402	2	Cleavage; by Ty1 protease By similarity
	Site	582 – 583	2	Cleavage; by Ty1 protease By similarity
	Site	1217 – 1218	2	Cleavage; by Ty1 protease By similarity
Amino acid modifications
	Modified residue	1006	1	Phosphothreonine Ref.6

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty1-ER1 Gag-Pol polyprotein [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 6EB17ED89FF1F6FB	FASTA	1,755	198,562
	10 20 30 40 50 60 MESQQLSQHS PISHGSACAS 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 430 440 450 460 470 480 TTEPIQLNNK HDLHLGQELT ESTVNHTNHS DDELPGHLLL DSGASRTLIR SAHHIHSASS 490 500 510 520 530 540 NPDINVVDAQ KRNIPINAIG DLQFHFQDNT KTSIKVLHTP NIAYDLLSLN ELAAVDITAC 550 560 570 580 590 600 FTKNVLERSD GTVLAPIVKY GDFYWVSKKY LLPSNISVPT INNVHTSEST RKYPYPFIHR 610 620 630 640 650 660 MLAHANAQTI RYSLKNNTIT YFNESDVDWS SAIDYQCPDC LIGKSTKHRH IKGSRLKYQN 670 680 690 700 710 720 SYEPFQYLHT DIFGPVHNLP KSAPSYFISF TDETTKFRWV YPLHDRREDS ILDVFTTILA 730 740 750 760 770 780 FIKNQFQASV LVIQMDRGSE YTNRTLHKFL EKNGITPCYT TTADSRAHGV AERLNRTLLD 790 800 810 820 830 840 DCRTQLQCSG LPNHLWFSAI EFSTIVRNSL ASPKSKKSAR QHAGLAGLDI STLLPFGQPV 850 860 870 880 890 900 IVNDHNPNSK IHPRGIPGYA LHPSRNSYGY IIYLPSLKKT VDTTNYVILQ GKESRLDQFN 910 920 930 940 950 960 YDALTFDEDL NRLTASYQSF IASNEIQQSD DLNIESDHDF QSDIELHPEQ PRNVLSKAVS 970 980 990 1000 1010 1020 PTDSTPPSTH TEDSKRVSKT NIRAPREVDP NISESNILPS KKRSSTPQIS NIESTGSGGM 1030 1040 1050 1060 1070 1080 HKLNVPLLAP MSQSNTHESS HASKSKDFRH SDSYSENETN HTNVPISSTG GTNNKTVPQI 1090 1100 1110 1120 1130 1140 SDQETEKRII HRSPSIDASP PENNSSHNIV PIKTPTTVSE QNTEESIIAD LPLPDLPPES 1150 1160 1170 1180 1190 1200 PTEFPDPFKE LPPINSHQTN SSLGGIGDSN AYTTINSKKR SLEDNETEIK VSRDTWNTKN 1210 1220 1230 1240 1250 1260 MRSLEPPRSK KRIHLIAAVK AVKSIKPIRT TLRYDEAITY NKDIKEKEKY IEAYHKEVNQ 1270 1280 1290 1300 1310 1320 LLKMKTWDTD EYYDRKEIDP KRVINSMFIF NKKRDGTHKA RFVARGDIQH PDTYDSGMQS 1330 1340 1350 1360 1370 1380 NTVHHYALMT SLSLALDNNY YITQLDISSA YLYADIKEEL YIRPPPHLGM NDKLIRLKKS 1390 1400 1410 1420 1430 1440 LYGLKQSGAN WYETIKSYLI KQCGMEEVRG WSCVFKNSQV TICLFVDDMI LFSKDLNANK 1450 1460 1470 1480 1490 1500 KIITTLKKQY DTKIINLGES DNEIQYDILG LEIKYQRGKY MKLGMENSLT EKIPKLNVPL 1510 1520 1530 1540 1550 1560 NPKGRKLSAP GQPGLYIDQD ELEIDEDEYK EKVHEMQKLI GLASYVGYKF RFDLLYYINT 1570 1580 1590 1600 1610 1620 LAQHILFPSR QVLDMTYELI QFMWDTRDKQ LIWHKNKPTE PDNKLVAISD ASYGNQPYYK 1630 1640 1650 1660 1670 1680 SQIGNIYLLN GKVIGGKSTK ASLTCTSTTE AEIHAISESV PLLNNLSYLI QELNKKPIIK 1690 1700 1710 1720 1730 1740 GLLTDSRSTI SIIKSTNEEK FRNRFFGTKA MRLRDEVSGN NLYVYYIETK KNIADVMTKP 1750 LPIKTFKLLT NKWIH
	Isoform Transposon Ty1-ER1 Gag polyprotein [UniParc]. See P0CX71.		–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(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]	"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.
[5]	"Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1 element." Wilhelm F.-X., Wilhelm M., Gabriel A. Cytogenet. Genome Res. 110:269-287(2005) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW, DOMAINS.
[6]	"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-1006, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U18917 Genomic DNA. Translation: AAB64665.1. BK006939 Genomic DNA. Translation: DAA07797.1.
PIR	S50641.
RefSeq	NP_011064.3. NM_001179028.3.
3D structure databases
ProteinModelPortal	Q03612.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-8790N.
IntAct	Q03612. 10 interactions.
MINT	MINT-692519.
STRING	4932.YER138C.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YER138C; YER138C; YER138C.
GeneID	856879.
KEGG	sce:YER138C. sce:YER140W.
Organism-specific databases
CYGD	YER138c.
SGD	S000000940. YER138C.
Phylogenomic databases
GeneTree	ENSGT00660000095717.
HOGENOM	HOG000280731.
Gene expression databases
ArrayExpress	Q03612.
Genevestigator	Q03612.
Family and domain databases
InterPro	IPR001584. Integrase_cat-core. IPR001969. Peptidase_aspartic_AS. IPR015820. Retrotransposon_Ty1A_N. IPR012337. RNaseH-like_dom. IPR013103. RVT_2. [Graphical view]
Pfam	PF00665. rve. 1 hit. PF07727. RVT_2. 1 hit. PF01021. TYA. 1 hit. [Graphical view]
SUPFAM	SSF53098. RNaseH_fold. 1 hit.
PROSITE	PS00141. ASP_PROTEASE. 1 hit. PS50994. INTEGRASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	983260.

Entry information

Entry name

YE11B_YEAST

Accession

Primary (citable) accession number: Q03612
Secondary accession number(s): D3DM43

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	November 1, 1996
Last modified:	April 3, 2013
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program