YP41B_YEAST
ID YP41B_YEAST Reviewed; 1104 AA.
AC A0A0B7P3V8;
DT 14-OCT-2015, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2015, sequence version 2.
DT 03-AUG-2022, entry version 35.
DE RecName: Full=Transposon Ty4-P Gag-Pol polyprotein;
DE AltName: Full=TY4A-TY4B;
DE AltName: Full=Transposon Ty4 TYA-TYB polyprotein;
DE Includes:
DE RecName: Full=Capsid protein;
DE Short=CA;
DE Includes:
DE RecName: Full=Ty4 protease;
DE Short=PR;
DE EC=3.4.23.-;
DE Includes:
DE RecName: Full=Integrase;
DE Short=IN;
DE Includes:
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;
GN Name=TY4B-P; Synonyms=YPLCTy4-1 POL;
GN OrderedLocusNames=YPL060C-A {ECO:0000312|SGD:S000007388};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
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 [3]
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 [4]
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
CC retrotransposons dimeric RNA genome. {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
CC ends. {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. {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;
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;
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 -!- 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. {ECO:0000250}.
CC -!- PTM: Proteolytically processed into capsid protein (CA), Ty4 protease
CC (PR), integrase (IN) and reverse transcriptase/ribonuclease H (RT)
CC proteins (By similarity). Initially, virus-like particles (VLPs) are
CC composed of the structural unprocessed proteins Gag and Gag-Pol, and
CC also contain the host initiator methionine tRNA (tRNA(i)-Met) which
CC serves as a primer for minus-strand DNA synthesis, and a dimer of
CC genomic Ty RNA. Processing of the polyproteins occurs within the
CC particle and proceeds by an ordered pathway, called maturation. First,
CC the protease (PR) is released by autocatalytic cleavage of the Gag-Pol
CC polyprotein, and this cleavage is a prerequisite for subsequent
CC processing at the remaining sites to release the mature structural and
CC catalytic proteins. Maturation takes place prior to the RT reaction and
CC is required to produce transposition-competent VLPs. {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. Ty4 retrotransposons belong
CC to the copia elements (pseudoviridae).
CC -!- CAUTION: Could be the product of a pseudogene. Transposon Ty4-P
CC (YPLCTy4-1) contains a frameshift at position 1105, which disrupts the
CC ORF coding for protein TY4B. It is probably not functional.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=DAA64692.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; BK006949; DAA64692.1; ALT_SEQ; Genomic_DNA.
DR RefSeq; NP_001291944.1; NM_001305015.2.
DR AlphaFoldDB; A0A0B7P3V8; -.
DR GeneID; 856047; -.
DR KEGG; sce:YPL060C-A; -.
DR SGD; S000007388; YPL060C-A.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; A0A0B7P3V8; protein.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
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:0032196; P:transposition; IEA:UniProtKB-KW.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF00665; rve; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
PE 5: Uncertain;
KW Aspartyl protease; ATP-binding; Coiled coil; Cytoplasm; DNA integration;
KW DNA recombination; DNA-binding; DNA-directed DNA polymerase; Endonuclease;
KW Hydrolase; Magnesium; Metal-binding; Nuclease; Nucleotide-binding;
KW Nucleotidyltransferase; Nucleus; Protease; Reference proteome; RNA-binding;
KW RNA-directed DNA polymerase; Transferase; Transposable element;
KW Transposition; Viral release from host cell; Virion maturation; Zinc;
KW Zinc-finger.
FT CHAIN 1..1104
FT /note="Transposon Ty4-P Gag-Pol polyprotein"
FT /id="PRO_0000434006"
FT DOMAIN 619..786
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT REGION 381..501
FT /note="Ty4 protease"
FT REGION 539..599
FT /note="Integrase-type zinc finger-like"
FT COILED 48..112
FT /evidence="ECO:0000255"
FT ACT_SITE 414
FT /note="For protease activity; shared with dimeric partner"
FT /evidence="ECO:0000250"
FT BINDING 630
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 695
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
SQ SEQUENCE 1104 AA; 127189 MW; E6D690A8CCD69B8C CRC64;
MATPVRDETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVKQ YQRNLNRFKT
ILNGLKAEEE KLSETDDIQM LAEKLLKLGE TIDKVENRIV DLVEKIQLLE TNENNNILHE
HIDATGTYYL FDTLTSTNKR FYPKDCVFDY RTNNVENIPI LLNNFKKFIK KYQFDDVFEN
DIIEIDPREN EILCKIIKEG LGESLDIMNT NTTDIFRIID GLKNKYRSLH GRDVRIRAWE
KVLVDTTCRN SALLMNKLQK LVLMEKWIFS KCCQDCPNLK DYLQEAIMGT LHESLRNSVK
QRLYNIPHNV GINHEEFLIN TVIETVIDLS PIADDQIENS CMYCKSVFHC SINCKKKPNR
ELRPDSTNFS KTYYLQGAQR QQQLKSSAKE QKSWNKTQKK SNKVYNSKKL VIIDTGSGVN
ITNDKTLLHN YEDSNRSTRF FGIGKNSSVS VKGYGYIKIK NGHNNTDNKC LLTYYVPEEE
STIISCYDLA KKTKMVLSRK YTRLGNKIIK IKTKIVNGVI HVKMNELIER PSDDSKINAI
KPTSSPGFKL NKRSITLEDA HKRMGHTGIQ QIENSIKHNH YEESLDLIKE PNEFWCQTCK
ISKATKRNHY TGSMNNHSTD HEPGSSWCMD IFGPVSSSNA DTKRYMLIMV DNNTRYCMTS
THFNKNAETI LAQIRKNIQY VETQFDRKVR EINSDRGTEF TNDQIEEYFI SKGIHHILTS
TQDHAANGRA ERYIRTIVTD ATTLLRQSNL RVKFWEYAVT SATNIRNCLE HKSTGKLPLK
AISRQPVTVR LMSFLPFGEK GIIWNHNHKK LKPSGLPSII LCKDPNSYGY KFFIPSKNKI
VTSDNYTIPN YTMDGRVRNT QNIYKSHQFS SHNDNEEDQI ETVTNLCEAL ENYEDDNKPI
TRLEDLFTEE ELSQIDSNAK YPSPSNNLEG DLDYVFSDVE ESGDYDVESE LSTTNTSIST
DKNKILSNKD FNSELASTEI SISEIDKKGL INTSHIDEDK YDEKVHRIPS IIQEKLVGSK
NTIKINDENR ISDRIRSKNI GSILNTGLSR CVDITDESIT NKDESMHNAK PELIQEQFNK
TNHETSFPKE GSIGTKCKIP KYRQ
