YI31B_YEAST
ID YI31B_YEAST Reviewed; 1498 AA.
AC Q7LHG5; D6VVK4; Q04717; Q04722; Q05350;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-MAR-2007, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Transposon Ty3-I Gag-Pol polyprotein;
DE AltName: Full=Gag3-Pol3;
DE AltName: Full=Transposon Ty3-2 TYA-TYB polyprotein;
DE Contains:
DE RecName: Full=Capsid protein;
DE Short=CA;
DE AltName: Full=p24;
DE Contains:
DE RecName: Full=Spacer peptide p3;
DE Contains:
DE RecName: Full=Nucleocapsid protein p11;
DE Short=NC;
DE Contains:
DE RecName: Full=Ty3 protease;
DE Short=PR;
DE EC=3.4.23.-;
DE AltName: Full=p16;
DE Contains:
DE RecName: Full=Spacer peptide J;
DE Contains:
DE RecName: Full=Reverse transcriptase/ribonuclease H;
DE Short=RT;
DE Short=RT-RH;
DE EC=2.7.7.49;
DE EC=2.7.7.7;
DE EC=3.1.26.4;
DE AltName: Full=p55;
DE Contains:
DE RecName: Full=Integrase p52;
DE Short=IN;
DE Contains:
DE RecName: Full=Integrase p49;
DE Short=IN;
GN Name=TY3B-I; Synonyms=YILWTy3-1 POL; OrderedLocusNames=YIL082W-A;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2854194; DOI=10.1128/mcb.8.12.5245-5256.1988;
RA Hansen L.J., Chalker D.L., Sandmeyer S.B.;
RT "Ty3, a yeast retrotransposon associated with tRNA genes, has homology to
RT animal retroviruses.";
RL Mol. Cell. Biol. 8:5245-5256(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169870;
RA Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
RA Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E.,
RA Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C.,
RA Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V.,
RA Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
RL Nature 387:84-87(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP FUNCTION.
RX PubMed=2159534; DOI=10.1128/jvi.64.6.2599-2607.1990;
RA Hansen L.J., Sandmeyer S.B.;
RT "Characterization of a transpositionally active Ty3 element and
RT identification of the Ty3 integrase protein.";
RL J. Virol. 64:2599-2607(1990).
RN [5]
RP NOMENCLATURE.
RX PubMed=9582191; DOI=10.1101/gr.8.5.464;
RA Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.;
RT "Transposable elements and genome organization: a comprehensive survey of
RT retrotransposons revealed by the complete Saccharomyces cerevisiae genome
RT sequence.";
RL Genome Res. 8:464-478(1998).
RN [6]
RP REVIEW.
RX PubMed=16093660; DOI=10.1159/000084940;
RA Lesage P., Todeschini A.L.;
RT "Happy together: the life and times of Ty retrotransposons and their
RT hosts.";
RL Cytogenet. Genome Res. 110:70-90(2005).
CC -!- FUNCTION: Capsid protein (CA) is the structural component of the virus-
CC like particle (VLP), forming the shell that encapsulates the genomic
CC RNA-nucleocapsid complex. {ECO:0000250}.
CC -!- FUNCTION: Nucleocapsid protein p11 (NC) forms the nucleocore that coats
CC the retro-elements dimeric RNA. Binds these RNAs through its zinc
CC fingers (By similarity). Promotes primer tRNA(i)-Met annealing to the
CC multipartite primer-binding site (PBS), dimerization of Ty3 RNA and
CC initiation of reverse transcription (By similarity). {ECO:0000250}.
CC -!- FUNCTION: The aspartyl protease (PR) mediates the proteolytic cleavages
CC of the Gag and Gag-Pol polyproteins after assembly of the VLP.
CC {ECO:0000250}.
CC -!- FUNCTION: Reverse transcriptase/ribonuclease H (RT) is a
CC multifunctional enzyme that catalyzes the conversion of the retro-
CC elements RNA genome into dsDNA within the VLP. The enzyme displays a
CC DNA polymerase activity that can copy either DNA or RNA templates, and
CC a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-
CC DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA
CC primers. The conversion leads to a linear dsDNA copy of the
CC retrotransposon that includes long terminal repeats (LTRs) at both ends
CC (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Integrase (IN) targets the VLP to the nucleus, where a
CC subparticle preintegration complex (PIC) containing at least integrase
CC and the newly synthesized dsDNA copy of the retrotransposon must
CC transit the nuclear membrane. Once in the nucleus, integrase performs
CC the integration of the dsDNA into the host genome (By similarity).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.49; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC -!- SUBUNIT: The protease is a homodimer, whose active site consists of two
CC apposed aspartic acid residues. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Ribosomal frameshifting; Named isoforms=2;
CC Comment=The Gag-Pol polyprotein is generated by a +1 ribosomal
CC frameshift.;
CC Name=Transposon Ty3-I Gag-Pol polyprotein;
CC IsoId=Q7LHG5-1; Sequence=Displayed;
CC Name=Transposon Ty3-I Gag polyprotein;
CC IsoId=Q99219-1; Sequence=External;
CC -!- DOMAIN: Integrase core domain contains the D-x(n)-D-x(35)-E motif,
CC named for the phylogenetically conserved glutamic acid and aspartic
CC acid residues and the invariant 35 amino acid spacing between the
CC second and third acidic residues. Each acidic residue of the D,D(35)E
CC motif is independently essential for the 3'-processing and strand
CC transfer activities of purified integrase protein (By similarity).
CC {ECO:0000250}.
CC -!- PTM: Initially, virus-like particles (VLPs) are composed of the
CC structural unprocessed proteins Gag and Gag-Pol, and also contain the
CC host initiator methionine tRNA (tRNA(i)-Met) which serves as a primer
CC for minus-strand DNA synthesis, and a dimer of genomic Ty RNA.
CC Processing of the polyproteins occurs within the particle and proceeds
CC by an ordered pathway, called maturation. First, the protease (PR) is
CC released by autocatalytic cleavage of the Gag-Pol polyprotein, and this
CC cleavage is a prerequisite for subsequent processing at the remaining
CC sites to release the mature structural and catalytic proteins.
CC Maturation takes place prior to the RT reaction and is required to
CC produce transposition-competent VLPs (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: Retrotransposons are mobile genetic entities that are
CC able to replicate via an RNA intermediate and a reverse transcription
CC step. In contrast to retroviruses, retrotransposons are non-infectious,
CC lack an envelope and remain intracellular. Ty3 retrotransposons belong
CC to the gypsy-like elements (metaviridae).
CC -!- MISCELLANEOUS: In contrast to Ty3-1 (Ty3-G), Ty3-2 (Ty3-I) is a
CC transpositionally inactive element. The Ty3-2 ORF is truncated by the
CC deletion of a single nucleotide, which causes a frameshift mutation
CC when compared with Ty3-1.
CC -!- MISCELLANEOUS: [Isoform Transposon Ty3-I Gag-Pol polyprotein]: Produced
CC by +1 ribosomal frameshifting between codon Ala-285 and Val-286 of the
CC YIL082W ORF.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA35184.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA86713.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=DAA08470.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; M23367; AAA35184.1; ALT_SEQ; Genomic_DNA.
DR EMBL; Z46728; CAA86713.1; ALT_SEQ; Genomic_DNA.
DR EMBL; Z37997; CAA86090.1; -; Genomic_DNA.
DR EMBL; BK006942; DAA08470.1; ALT_SEQ; Genomic_DNA.
DR PIR; S53577; S53577.
DR RefSeq; NP_012184.1; NM_001181434.4.
DR PDB; 6R22; EM; 5.50 A; A/B=1-309.
DR PDB; 6R23; EM; 4.90 A; A/B=1-309.
DR PDB; 6R24; EM; 7.50 A; A/B/C/D/E/F/G/H/I=1-309.
DR PDBsum; 6R22; -.
DR PDBsum; 6R23; -.
DR PDBsum; 6R24; -.
DR AlphaFoldDB; Q7LHG5; -.
DR SMR; Q7LHG5; -.
DR BioGRID; 34910; 6.
DR IntAct; Q7LHG5; 3.
DR MINT; Q7LHG5; -.
DR STRING; 4932.YIL082W-A; -.
DR MEROPS; A02.022; -.
DR PaxDb; Q7LHG5; -.
DR PRIDE; Q7LHG5; -.
DR GeneID; 854728; -.
DR KEGG; sce:YIL082W-A; -.
DR SGD; S000003537; YIL082W-A.
DR eggNOG; KOG0017; Eukaryota.
DR HOGENOM; CLU_000384_9_7_1; -.
DR InParanoid; Q7LHG5; -.
DR Proteomes; UP000002311; Chromosome IX.
DR RNAct; Q7LHG5; protein.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0000943; C:retrotransposon nucleocapsid; ISS:SGD.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; ISS:SGD.
DR GO; GO:0008233; F:peptidase activity; ISS:SGD.
DR GO; GO:0004540; F:ribonuclease activity; ISS:SGD.
DR GO; GO:0003723; F:RNA binding; ISS:SGD.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; ISS:SGD.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0032197; P:transposition, RNA-mediated; ISS:SGD.
DR Gene3D; 2.40.70.10; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.30.70.270; -; 2.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR041588; Integrase_H2C2.
DR InterPro; IPR024650; Peptidase_A2B.
DR InterPro; IPR021109; Peptidase_aspartic_dom_sf.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR000477; RT_dom.
DR InterPro; IPR041577; RT_RNaseH_2.
DR InterPro; IPR045358; Ty3_capsid.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR Pfam; PF17921; Integrase_H2C2; 1.
DR Pfam; PF12384; Peptidase_A2B; 1.
DR Pfam; PF17919; RT_RNaseH_2; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF00078; RVT_1; 1.
DR Pfam; PF19259; Ty3_capsid; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF50630; SSF50630; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR SUPFAM; SSF57756; SSF57756; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
DR PROSITE; PS50878; RT_POL; 1.
DR PROSITE; PS50158; ZF_CCHC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aspartyl protease; ATP-binding; Cytoplasm; DNA integration;
KW DNA recombination; DNA-binding; DNA-directed DNA polymerase; Endonuclease;
KW Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotide-binding; Nucleotidyltransferase; Nucleus; Protease;
KW Reference proteome; Ribosomal frameshifting; RNA-binding;
KW RNA-directed DNA polymerase; Transferase; Transposable element;
KW Viral release from host cell; Virion maturation; Zinc; Zinc-finger.
FT CHAIN 1..1498
FT /note="Transposon Ty3-I Gag-Pol polyprotein"
FT /id="PRO_0000279367"
FT CHAIN 1..207
FT /note="Capsid protein"
FT /id="PRO_0000279368"
FT PEPTIDE 208..233
FT /note="Spacer peptide p3"
FT /id="PRO_0000279369"
FT CHAIN 234..309
FT /note="Nucleocapsid protein p11"
FT /id="PRO_0000279370"
FT CHAIN 310..442
FT /note="Ty3 protease"
FT /id="PRO_0000279371"
FT PEPTIDE 443..561
FT /note="Spacer peptide J"
FT /evidence="ECO:0000255"
FT /id="PRO_0000279372"
FT CHAIN 562..1037
FT /note="Reverse transcriptase/ribonuclease H"
FT /id="PRO_0000279373"
FT CHAIN 1038..1498
FT /note="Integrase p52"
FT /id="PRO_0000279374"
FT CHAIN 1064..1498
FT /note="Integrase p49"
FT /id="PRO_0000279375"
FT DOMAIN 646..823
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT DOMAIN 919..1037
FT /note="RNase H Ty3/gyspy-type"
FT DOMAIN 1185..1350
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT ZN_FING 265..282
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 470..490
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1132..1171
FT /note="Integrase-type zinc finger-like"
FT COMPBIAS 476..490
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 336
FT /note="For protease activity; shared with dimeric partner"
FT /evidence="ECO:0000250"
FT BINDING 712
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 774
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 775
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 1201
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000250"
FT BINDING 1262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000250"
FT SITE 207..208
FT /note="Cleavage; by Ty3 protease"
FT SITE 233..234
FT /note="Cleavage; by Ty3 protease"
FT SITE 309..310
FT /note="Cleavage; by Ty3 protease"
FT SITE 442..443
FT /note="Cleavage; by Ty3 protease"
FT /evidence="ECO:0000255"
FT SITE 561..562
FT /note="Cleavage; by Ty3 protease"
FT SITE 1037..1038
FT /note="Cleavage; by Ty3 protease"
FT SITE 1063..1064
FT /note="Cleavage; by Ty3 protease; partial"
FT CONFLICT 502
FT /note="G -> A (in Ref. 1; AAA35184)"
FT /evidence="ECO:0000305"
SQ 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
