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Transposon Ty3-I Gag-Pol polyprotein (Gag3-Pol3) (Transposon Ty3-2 TYA-TYB polyprotein) [Cleaved into: Capsid protein (CA) (p24); Spacer peptide p3; Nucleocapsid protein p11 (NC); Ty3 protease (PR) (EC 3.4.23.-) (p16); Spacer peptide J; Reverse transcriptase/ribonuclease H (RT) (RT-RH) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p55); Integrase p52 (IN); Integrase p49 (IN)]

 YI31B_YEAST             Reviewed;        1498 AA.
Q7LHG5; D6VVK4; Q04717; Q04722; Q05350;
06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
06-MAR-2007, sequence version 2.
28-MAR-2018, entry version 122.
RecName: Full=Transposon Ty3-I Gag-Pol polyprotein;
AltName: Full=Gag3-Pol3;
AltName: Full=Transposon Ty3-2 TYA-TYB polyprotein;
Contains:
RecName: Full=Capsid protein;
Short=CA;
AltName: Full=p24;
Contains:
RecName: Full=Spacer peptide p3;
Contains:
RecName: Full=Nucleocapsid protein p11;
Short=NC;
Contains:
RecName: Full=Ty3 protease;
Short=PR;
EC=3.4.23.-;
AltName: Full=p16;
Contains:
RecName: Full=Spacer peptide J;
Contains:
RecName: Full=Reverse transcriptase/ribonuclease H;
Short=RT;
Short=RT-RH;
EC=2.7.7.49;
EC=2.7.7.7;
EC=3.1.26.4;
AltName: Full=p55;
Contains:
RecName: Full=Integrase p52;
Short=IN;
Contains:
RecName: Full=Integrase p49;
Short=IN;
Name=TY3B-I; Synonyms=YILWTy3-1 POL; OrderedLocusNames=YIL082W-A;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=2854194; DOI=10.1128/MCB.8.12.5245;
Hansen L.J., Chalker D.L., Sandmeyer S.B.;
"Ty3, a yeast retrotransposon associated with tRNA genes, has homology
to animal retroviruses.";
Mol. Cell. Biol. 8:5245-5256(1988).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169870;
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N.,
Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G.,
Moule S., Odell C., Pearson D., Rajandream M.A., Rice P., Rowley N.,
Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
Nature 387:84-87(1997).
[3]
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).
[4]
FUNCTION.
PubMed=2159534;
Hansen L.J., Sandmeyer S.B.;
"Characterization of a transpositionally active Ty3 element and
identification of the Ty3 integrase protein.";
J. Virol. 64:2599-2607(1990).
[5]
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).
[6]
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).
-!- FUNCTION: Capsid protein (CA) is the structural component of the
virus-like particle (VLP), forming the shell that encapsulates the
genomic RNA-nucleocapsid complex. {ECO:0000250}.
-!- FUNCTION: Nucleocapsid protein p11 (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
(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). {ECO:0000255|PROSITE-ProRule:PRU00405}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester.
-!- SUBUNIT: The protease is a homodimer, whose active site consists
of two apposed aspartic acid residues. {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.;
Name=Transposon Ty3-I Gag-Pol polyprotein;
IsoId=Q7LHG5-1; Sequence=Displayed;
Note=Produced by +1 ribosomal frameshifting between codon
Ala-285 and Val-286 of the YIL082W ORF.;
Name=Transposon Ty3-I Gag polyprotein;
IsoId=Q99219-1; Sequence=External;
Note=Produced by conventional translation.;
-!- 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, and this cleavage is a prerequisite for subsequent
processing 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. Ty3
retrotransposons belong to the gypsy-like elements (metaviridae).
-!- MISCELLANEOUS: In contrast to Ty3-1 (Ty3-G), Ty3-2 (Ty3-I) is a
transpositionally inactive element. The Ty3-2 ORF is truncated by
the deletion of a single nucleotide, which causes a frameshift
mutation when compared with Ty3-1.
-!- SEQUENCE CAUTION:
Sequence=AAA35184.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=CAA86713.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=DAA08470.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; M23367; AAA35184.1; ALT_SEQ; Genomic_DNA.
EMBL; Z46728; CAA86713.1; ALT_SEQ; Genomic_DNA.
EMBL; Z37997; CAA86090.1; -; Genomic_DNA.
EMBL; BK006942; DAA08470.1; ALT_SEQ; Genomic_DNA.
PIR; S53577; S53577.
RefSeq; NP_012184.1; NM_001181434.4.
ProteinModelPortal; Q7LHG5; -.
SMR; Q7LHG5; -.
BioGrid; 34910; 5.
IntAct; Q7LHG5; 10.
MINT; Q7LHG5; -.
STRING; 4932.YIL082W-A; -.
PaxDb; Q7LHG5; -.
PRIDE; Q7LHG5; -.
GeneID; 854728; -.
KEGG; sce:YIL082W-A; -.
EuPathDB; FungiDB:YIL082W-A; -.
SGD; S000003537; YIL082W-A.
HOGENOM; HOG000172599; -.
InParanoid; Q7LHG5; -.
KO; K07497; -.
OrthoDB; EOG092C0KYC; -.
Proteomes; UP000002311; Chromosome IX.
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: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:0008270; F:zinc ion binding; IEA:InterPro.
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; 2.40.70.10; -; 1.
Gene3D; 3.30.420.10; -; 1.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR024650; Peptidase_A2B.
InterPro; IPR021109; Peptidase_aspartic_dom_sf.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
InterPro; IPR000477; RT_dom.
InterPro; IPR001878; Znf_CCHC.
InterPro; IPR036875; Znf_CCHC_sf.
Pfam; PF12384; Peptidase_A2B; 1.
Pfam; PF00665; rve; 1.
Pfam; PF00078; RVT_1; 1.
SMART; SM00343; ZnF_C2HC; 1.
SUPFAM; SSF50630; SSF50630; 1.
SUPFAM; SSF53098; SSF53098; 1.
SUPFAM; SSF57756; SSF57756; 1.
PROSITE; PS50994; INTEGRASE; 1.
PROSITE; PS50878; RT_POL; 1.
PROSITE; PS50158; ZF_CCHC; 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; Protease; Reference proteome;
Ribosomal frameshifting; RNA-binding; RNA-directed DNA polymerase;
Transferase; Transposable element; Viral release from host cell;
Virion maturation; Zinc; Zinc-finger.
CHAIN 1 1498 Transposon Ty3-I Gag-Pol polyprotein.
/FTId=PRO_0000279367.
CHAIN 1 207 Capsid protein.
/FTId=PRO_0000279368.
PEPTIDE 208 233 Spacer peptide p3.
/FTId=PRO_0000279369.
CHAIN 234 309 Nucleocapsid protein p11.
/FTId=PRO_0000279370.
CHAIN 310 442 Ty3 protease.
/FTId=PRO_0000279371.
PEPTIDE 443 561 Spacer peptide J. {ECO:0000255}.
/FTId=PRO_0000279372.
CHAIN 562 1037 Reverse transcriptase/ribonuclease H.
/FTId=PRO_0000279373.
CHAIN 1038 1498 Integrase p52.
/FTId=PRO_0000279374.
CHAIN 1064 1498 Integrase p49.
/FTId=PRO_0000279375.
DOMAIN 646 823 Reverse transcriptase.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
DOMAIN 919 1037 RNase H Ty3/gyspy-type.
DOMAIN 1185 1350 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
ZN_FING 265 282 CCHC-type. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
REGION 1132 1171 Integrase-type zinc finger-like.
ACT_SITE 336 336 For protease activity; shared with
dimeric partner. {ECO:0000250}.
METAL 712 712 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 774 774 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 775 775 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 1201 1201 Magnesium; catalytic; for integrase
activity. {ECO:0000250}.
METAL 1262 1262 Magnesium; catalytic; for integrase
activity. {ECO:0000250}.
SITE 207 208 Cleavage; by Ty3 protease.
SITE 233 234 Cleavage; by Ty3 protease.
SITE 309 310 Cleavage; by Ty3 protease.
SITE 442 443 Cleavage; by Ty3 protease. {ECO:0000255}.
SITE 561 562 Cleavage; by Ty3 protease.
SITE 1037 1038 Cleavage; by Ty3 protease.
SITE 1063 1064 Cleavage; by Ty3 protease; partial.
CONFLICT 502 502 G -> A (in Ref. 1; AAA35184).
{ECO:0000305}.
SEQUENCE 1498 AA; 172369 MW; 4E51C3EFBDEFD7E4 CRC64;
MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND
ASRIVYCRRH LLNPAAQWAN DFVQEQGILE ITFDTFIQGL YQHFYKPPDI NKIFNAITQL
SEAKLGIERL NQRFRKIWDR MPPDFMTEKA AIMTYTRLLT KETYNIVRMH KPETLKDAME
EAYQTTALTE RFFPGFELDA DGDTIIGATT HLQEEYDSDY DSEDNLTQNR YVHTVRTRRS
YNKPMSNHRN RRNNNASREE CIKNRLCFYC KKEGHRLNEC RARKAVLTDL ELESKDQQTL
FIKTLPIVHY IAIPEMDNTA EKTIKIQNTK VKTLFDSGSP TSFIRRDIVE LLKYEIYETP
PLRFRGFVAT KSAVTSEAVT IDLKINDLQI TLAAYILDNM DYQLLIGNPI LRRYPKILHT
VLNTRESPDS LKPKTYRSET VNNVRTYSAG NRGNPRNIKL SFAPTILEAT DPKSAGNRGN
PRNTKLSLAP TILEATDPKS AGNRGDSRTK TLSLATTTPA AIDPLTTLDN PGSTQSTFAQ
FPIPEEASIL EEDGKYSNVV STIQSVEPNA TDHSNKDTFC TLPVWLQQKY REIIRNDLPP
RPADINNIPV KHDIEIKPGA RLPRLQPYHV TEKNEQEINK IVQKLLDNKF IVPSKSPCSS
PVVLVPKKDG TFRLCVDYRT LNKATISDPF PLPRIDNLLS RIGNAQIFTT LDLHSGYHQI
PMEPKDRYKT AFVTPSGKYE YTVMPFGLVN APSTFARYMA DTFRDLRFVN VYLDDILIFS
ESPEEHWKHL DTVLERLKNE NLIVKKKKCK FASEETEFLG YSIGIQKIAP LQHKCAAIRD
FPTPKTVKQA QRFLGMINYY RRFIPNCSKI AQPIQLFICD KSQWTEKQDK AIEKLKAALC
NSPVLVPFNN KANYRLTTDA SKDGIGAVLE EVDNKNKLVG VVGYFSKSLE SAQKNYPAGE
LELLGIIKAL HHFRYMLHGK HFTLRTDHIS LLSLQNKNEP ARRVQRWLDD LATYDFTLEY
LAGPKNVVAD AISRAIYTIT PETSRPIDTE SWKSYYKSDP LCSAVLIHMK ELTQHNVTPE
DMSAFRSYQK KLELSETFRK NYSLEDEMIY YQDRLVVPIK QQNAVMRLYH DHTLFGGHFG
VTVTLAKISP IYYWPKLQHS IIQYIRTCVQ CQLIKSHRPR LHGLLQPLPI AEGRWLDISM
DFVTGLPPTS NNLNMILVVV DRFSKRAHFI ATRKTLDATQ LIDLLFRYIF SYHGFPRTIT
SDRDVRMTAD KYQELTKRLG IKSTMSSANH PQTDGQSERT IQTLNRLLRA YVSTNIQNWH
VYLPQIEFVY NSTPTRTLGK SPFEIDLGYL PNTPAIKSDD EVNARSFTAV ELAKHLKALT
IQTKEQLEHA QIEMETNNNQ RRKPLLLNIG DHVLVHRDAY FKKGAYMKVQ QIYVGPFRVV
KKINDNAYEL DLNSHKKKHR VINVQFLKSL YTVQTRTQRI NQSAPLRELR EHTKLLHS


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