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Transposon Ty1-ER1 Gag-Pol polyprotein (Gag-Pol-p199) (TY1A-TY1B) (Transposon Ty1 TYA-TYB polyprotein) (p190) [Cleaved into: Capsid protein (CA) (Gag-p45) (p54); Ty1 protease (PR) (EC 3.4.23.-) (Pol-p20) (p23); Integrase (IN) (Pol-p71) (p84) (p90); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (Pol-p63) (p60)]

 YE11B_YEAST             Reviewed;        1755 AA.
Q03612; D3DM43;
06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
25-OCT-2017, entry version 137.
RecName: Full=Transposon Ty1-ER1 Gag-Pol polyprotein;
AltName: Full=Gag-Pol-p199;
AltName: Full=TY1A-TY1B;
AltName: Full=Transposon Ty1 TYA-TYB polyprotein;
AltName: Full=p190;
Contains:
RecName: Full=Capsid protein;
Short=CA;
AltName: Full=Gag-p45;
AltName: Full=p54;
Contains:
RecName: Full=Ty1 protease;
Short=PR;
EC=3.4.23.-;
AltName: Full=Pol-p20;
AltName: Full=p23;
Contains:
RecName: Full=Integrase;
Short=IN;
AltName: Full=Pol-p71;
AltName: Full=p84;
AltName: Full=p90;
Contains:
RecName: Full=Reverse transcriptase/ribonuclease H;
Short=RT;
EC=2.7.7.49;
EC=2.7.7.7;
EC=3.1.26.4;
AltName: Full=Pol-p63;
AltName: Full=p60;
Name=TY1B-ER1; Synonyms=YERCTy1-1 POL; OrderedLocusNames=YER138C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169868;
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.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
Nature 387:78-81(1997).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
NOMENCLATURE.
PubMed=9582191;
Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.;
"Transposable elements and genome organization: a comprehensive survey
of retrotransposons revealed by the complete Saccharomyces cerevisiae
genome sequence.";
Genome Res. 8:464-478(1998).
[4]
REVIEW.
PubMed=16093660; DOI=10.1159/000084940;
Lesage P., Todeschini A.L.;
"Happy together: the life and times of Ty retrotransposons and their
hosts.";
Cytogenet. Genome Res. 110:70-90(2005).
[5]
REVIEW, AND DOMAINS.
PubMed=16093680; DOI=10.1159/000084960;
Wilhelm F.-X., Wilhelm M., Gabriel A.;
"Reverse transcriptase and integrase of the Saccharomyces cerevisiae
Ty1 element.";
Cytogenet. Genome Res. 110:269-287(2005).
-!- 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). {ECO:0000250}.
-!- FUNCTION: The aspartyl protease (PR) mediates the proteolytic
cleavages of the Gag and Gag-Pol polyproteins after assembly of
the VLP. {ECO:0000250}.
-!- FUNCTION: 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).
{ECO:0000250}.
-!- FUNCTION: 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). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1).
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester.
-!- SUBUNIT: 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).
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=2;
Comment=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). {ECO:0000250};
Name=Transposon Ty1-ER1 Gag-Pol polyprotein;
IsoId=Q03612-1; Sequence=Displayed;
Note=Produced by +1 ribosomal frameshifting between codon
Leu-435 and Gly-436 of the YER137C-A ORF.;
Name=Transposon Ty1-ER1 Gag polyprotein;
IsoId=P0CX71-1; Sequence=External;
Note=Produced by conventional translation.;
-!- DOMAIN: The C-terminal RNA-binding region of CA is sufficient for
all its nucleocapsid-like chaperone activities. {ECO:0000250}.
-!- DOMAIN: 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,D(35)E motif is independently essential for the 3'-
processing and strand transfer activities of purified integrase
protein (By similarity). {ECO:0000250}.
-!- PTM: 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). {ECO:0000250}.
-!- 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).
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; U18917; AAB64665.1; -; Genomic_DNA.
EMBL; BK006939; DAA07797.1; -; Genomic_DNA.
PIR; S50641; S50641.
RefSeq; NP_011064.3; NM_001179028.4. [Q03612-1]
ProteinModelPortal; Q03612; -.
SMR; Q03612; -.
BioGrid; 36885; 14.
DIP; DIP-8790N; -.
IntAct; Q03612; 10.
MINT; MINT-692519; -.
STRING; 4932.YER138C; -.
iPTMnet; Q03612; -.
MaxQB; Q03612; -.
PRIDE; Q03612; -.
EnsemblFungi; YER138C; YER138C; YER138C. [Q03612-1]
GeneID; 856879; -.
KEGG; sce:YER138C; -.
EuPathDB; FungiDB:YER138C; -.
SGD; S000000940; YER138C.
GeneTree; ENSGT00900000141723; -.
HOGENOM; HOG000280731; -.
InParanoid; Q03612; -.
OrthoDB; EOG092C2F0T; -.
Proteomes; UP000002311; Chromosome V.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0000943; C:retrotransposon nucleocapsid; ISS:SGD.
GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; ISS:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008233; F:peptidase activity; ISS:SGD.
GO; GO:0004540; F:ribonuclease activity; ISS:SGD.
GO; GO:0003723; F:RNA binding; ISS:SGD.
GO; GO:0003964; F:RNA-directed DNA polymerase activity; ISS:SGD.
GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0032197; P:transposition, RNA-mediated; ISS:SGD.
Gene3D; 3.30.420.10; -; 1.
InterPro; IPR001969; Aspartic_peptidase_AS.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR015820; Retrotransposon_Ty1A_N.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
InterPro; IPR013103; RVT_2.
Pfam; PF00665; rve; 1.
Pfam; PF07727; RVT_2; 1.
Pfam; PF01021; TYA; 1.
SUPFAM; SSF53098; SSF53098; 1.
PROSITE; PS00141; ASP_PROTEASE; 1.
PROSITE; PS50994; INTEGRASE; 1.
3: Inferred from homology;
Aspartyl protease; ATP-binding; Complete proteome; Cytoplasm;
DNA integration; DNA recombination; DNA-binding;
DNA-directed DNA polymerase; Endonuclease; Hydrolase; Magnesium;
Metal-binding; Multifunctional enzyme; Nuclease; Nucleotide-binding;
Nucleotidyltransferase; Nucleus; Phosphoprotein; Protease;
Reference proteome; Ribosomal frameshifting; RNA-binding;
RNA-directed DNA polymerase; Transferase; Transposable element;
Transposition; Viral release from host cell; Virion maturation; Zinc;
Zinc-finger.
CHAIN 1 1755 Transposon Ty1-ER1 Gag-Pol polyprotein.
/FTId=PRO_0000279043.
CHAIN 1 401 Capsid protein. {ECO:0000250}.
/FTId=PRO_0000279044.
CHAIN 402 582 Ty1 protease. {ECO:0000250}.
/FTId=PRO_0000279045.
CHAIN 583 1217 Integrase. {ECO:0000250}.
/FTId=PRO_0000279046.
CHAIN 1218 1755 Reverse transcriptase/ribonuclease H.
{ECO:0000250}.
/FTId=PRO_0000279047.
DOMAIN 660 835 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
DOMAIN 1338 1476 Reverse transcriptase Ty1/copia-type.
DOMAIN 1610 1752 RNase H Ty1/copia-type.
REGION 299 401 RNA-binding. {ECO:0000250}.
REGION 583 640 Integrase-type zinc finger-like.
MOTIF 1178 1212 Bipartite nuclear localization signal.
{ECO:0000250}.
COMPBIAS 64 146 Pro-rich.
ACT_SITE 461 461 For protease activity; shared with
dimeric partner. {ECO:0000255|PROSITE-
ProRule:PRU10094}.
METAL 671 671 Magnesium; catalytic; for integrase
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 736 736 Magnesium; catalytic; for integrase
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1346 1346 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1427 1427 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1428 1428 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1610 1610 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1652 1652 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1685 1685 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
SITE 401 402 Cleavage; by Ty1 protease. {ECO:0000250}.
SITE 582 583 Cleavage; by Ty1 protease. {ECO:0000250}.
SITE 1217 1218 Cleavage; by Ty1 protease. {ECO:0000250}.
MOD_RES 416 416 Phosphoserine.
{ECO:0000250|UniProtKB:Q99231}.
SEQUENCE 1755 AA; 198562 MW; 6EB17ED89FF1F6FB CRC64;
MESQQLSQHS PISHGSACAS VTSKEVHTNQ DPLDVSASKT EECEKASTKA NSQQTTTPAS
SAVPENPHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG WSFYGHPSMI PYTPYQMSPM
YFPPGPQSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND
FPNWVKTYIK FLQNSNLGGI IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI
LSVDYTDIMK ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN
GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ QGSRNSKPNY
RRNLSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA HNVSTSNNSP STDNDSISKS
TTEPIQLNNK HDLHLGQELT ESTVNHTNHS DDELPGHLLL DSGASRTLIR SAHHIHSASS
NPDINVVDAQ KRNIPINAIG DLQFHFQDNT KTSIKVLHTP NIAYDLLSLN ELAAVDITAC
FTKNVLERSD GTVLAPIVKY GDFYWVSKKY LLPSNISVPT INNVHTSEST RKYPYPFIHR
MLAHANAQTI RYSLKNNTIT YFNESDVDWS SAIDYQCPDC LIGKSTKHRH IKGSRLKYQN
SYEPFQYLHT DIFGPVHNLP KSAPSYFISF TDETTKFRWV YPLHDRREDS ILDVFTTILA
FIKNQFQASV LVIQMDRGSE YTNRTLHKFL EKNGITPCYT TTADSRAHGV AERLNRTLLD
DCRTQLQCSG LPNHLWFSAI EFSTIVRNSL ASPKSKKSAR QHAGLAGLDI STLLPFGQPV
IVNDHNPNSK IHPRGIPGYA LHPSRNSYGY IIYLPSLKKT VDTTNYVILQ GKESRLDQFN
YDALTFDEDL NRLTASYQSF IASNEIQQSD DLNIESDHDF QSDIELHPEQ PRNVLSKAVS
PTDSTPPSTH TEDSKRVSKT NIRAPREVDP NISESNILPS KKRSSTPQIS NIESTGSGGM
HKLNVPLLAP MSQSNTHESS HASKSKDFRH SDSYSENETN HTNVPISSTG GTNNKTVPQI
SDQETEKRII HRSPSIDASP PENNSSHNIV PIKTPTTVSE QNTEESIIAD LPLPDLPPES
PTEFPDPFKE LPPINSHQTN SSLGGIGDSN AYTTINSKKR SLEDNETEIK VSRDTWNTKN
MRSLEPPRSK KRIHLIAAVK AVKSIKPIRT TLRYDEAITY NKDIKEKEKY IEAYHKEVNQ
LLKMKTWDTD EYYDRKEIDP KRVINSMFIF NKKRDGTHKA RFVARGDIQH PDTYDSGMQS
NTVHHYALMT SLSLALDNNY YITQLDISSA YLYADIKEEL YIRPPPHLGM NDKLIRLKKS
LYGLKQSGAN WYETIKSYLI KQCGMEEVRG WSCVFKNSQV TICLFVDDMI LFSKDLNANK
KIITTLKKQY DTKIINLGES DNEIQYDILG LEIKYQRGKY MKLGMENSLT EKIPKLNVPL
NPKGRKLSAP GQPGLYIDQD ELEIDEDEYK EKVHEMQKLI GLASYVGYKF RFDLLYYINT
LAQHILFPSR QVLDMTYELI QFMWDTRDKQ LIWHKNKPTE PDNKLVAISD ASYGNQPYYK
SQIGNIYLLN GKVIGGKSTK ASLTCTSTTE AEIHAISESV PLLNNLSYLI QELNKKPIIK
GLLTDSRSTI SIIKSTNEEK FRNRFFGTKA MRLRDEVSGN NLYVYYIETK KNIADVMTKP
LPIKTFKLLT NKWIH


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