YH11B_YEAST
ID YH11B_YEAST Reviewed; 1793 AA.
AC O13535; D3DLG6;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Transposon Ty1-H Gag-Pol polyprotein;
DE AltName: Full=Gag-Pol-p199;
DE AltName: Full=TY1A-TY1B;
DE AltName: Full=Transposon Ty1 TYA-TYB polyprotein;
DE AltName: Full=p190;
DE Contains:
DE RecName: Full=Capsid protein;
DE Short=CA;
DE AltName: Full=Gag-p45;
DE AltName: Full=p54;
DE Contains:
DE RecName: Full=Ty1 protease;
DE Short=PR;
DE EC=3.4.23.-;
DE AltName: Full=Pol-p20;
DE AltName: Full=p23;
DE Contains:
DE RecName: Full=Integrase;
DE Short=IN;
DE AltName: Full=Pol-p71;
DE AltName: Full=p84;
DE AltName: Full=p90;
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=Pol-p63;
DE AltName: Full=p60;
GN Name=TY1B-H; Synonyms=YHRCTy1-1 POL; OrderedLocusNames=YHR214C-B;
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=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
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).
RN [5]
RP REVIEW, AND DOMAINS.
RX PubMed=16093680; DOI=10.1159/000084960;
RA Wilhelm F.-X., Wilhelm M., Gabriel A.;
RT "Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1
RT element.";
RL Cytogenet. Genome Res. 110:269-287(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. The particles are assembled from
CC trimer-clustered units and there are holes in the capsid shells that
CC allow for the diffusion of macromolecules. CA has also nucleocapsid-
CC like chaperone activity, promoting primer tRNA(i)-Met annealing to the
CC multipartite primer-binding site (PBS), dimerization of Ty1 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;
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 capsid protein forms a homotrimer, from which the VLPs are
CC assembled. The protease is a homodimer, whose active site consists of
CC two apposed aspartic acid residues (By similarity). {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. The ratio of Gag:Gag-Pol varies between 20:1 and 5:1 (By
CC similarity). {ECO:0000250};
CC Name=Transposon Ty1-H Gag-Pol polyprotein;
CC IsoId=O13535-1; Sequence=Displayed;
CC Name=Transposon Ty1-H Gag polyprotein;
CC IsoId=P0C2I4-1; Sequence=External;
CC -!- DOMAIN: The C-terminal RNA-binding region of CA is sufficient for all
CC its nucleocapsid-like chaperone activities. {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 (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 yielding
CC capsid protein p45 and a Pol-p154 precursor protein. This cleavage is a
CC prerequisite for subsequent processing of Pol-p154 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. Ty1 retrotransposons belong
CC to the copia elements (pseudoviridae).
CC -!- MISCELLANEOUS: [Isoform Transposon Ty1-H Gag-Pol polyprotein]: Produced
CC by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the
CC YHR214C-C ORF.
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DR EMBL; U00029; AAB69744.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06910.1; -; Genomic_DNA.
DR PIR; S40969; S40969.
DR PIR; S52601; S52601.
DR RefSeq; NP_012086.1; NM_001181431.2. [O13535-1]
DR AlphaFoldDB; O13535; -.
DR BioGRID; 36648; 9.
DR IntAct; O13535; 3.
DR MINT; O13535; -.
DR iPTMnet; O13535; -.
DR PaxDb; O13535; -.
DR PRIDE; O13535; -.
DR GeneID; 856623; -.
DR KEGG; sce:YHR214C-B; -.
DR SGD; S000003534; YHR214C-B.
DR VEuPathDB; FungiDB:YHR214C-B; -.
DR eggNOG; KOG0017; Eukaryota.
DR HOGENOM; CLU_244151_0_0_1; -.
DR InParanoid; O13535; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; O13535; 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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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: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; 3.30.420.10; -; 1.
DR InterPro; IPR001969; Aspartic_peptidase_AS.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR013103; RVT_2.
DR InterPro; IPR015820; TYA.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF07727; RVT_2; 1.
DR Pfam; PF01021; TYA; 2.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS00141; ASP_PROTEASE; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
PE 3: Inferred from homology;
KW 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 Transposition; Viral release from host cell; Virion maturation; Zinc;
KW Zinc-finger.
FT CHAIN 1..1793
FT /note="Transposon Ty1-H Gag-Pol polyprotein"
FT /id="PRO_0000279074"
FT CHAIN 1..439
FT /note="Capsid protein"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279075"
FT CHAIN 440..620
FT /note="Ty1 protease"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279076"
FT CHAIN 621..1255
FT /note="Integrase"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279077"
FT CHAIN 1256..1793
FT /note="Reverse transcriptase/ribonuclease H"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279078"
FT DOMAIN 698..873
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT DOMAIN 1376..1514
FT /note="Reverse transcriptase Ty1/copia-type"
FT DOMAIN 1648..1790
FT /note="RNase H Ty1/copia-type"
FT REGION 1..84
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 126..174
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 337..439
FT /note="RNA-binding"
FT /evidence="ECO:0000250"
FT REGION 390..459
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 621..678
FT /note="Integrase-type zinc finger-like"
FT REGION 996..1208
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1216..1250
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000250"
FT COMPBIAS 1..67
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 131..164
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 398..412
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 413..459
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1007..1021
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1031..1053
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1078..1094
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1095..1118
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1132..1149
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1187..1208
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 499
FT /note="For protease activity; shared with dimeric partner"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10094"
FT BINDING 709
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 774
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 1384
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 1465
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 1466
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 1648
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 1690
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 1723
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for RNase H activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT SITE 439..440
FT /note="Cleavage; by Ty1 protease"
FT /evidence="ECO:0000250"
FT SITE 620..621
FT /note="Cleavage; by Ty1 protease"
FT /evidence="ECO:0000250"
FT SITE 1255..1256
FT /note="Cleavage; by Ty1 protease"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1793 AA; 202817 MW; 1DA6A07E10E0A2CB CRC64;
MESQQLSNYP HISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA NSQQTTTPAS
SAVPENLHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG WSFYGHPSMI PYTPYQMSPM
YFPPGPQSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND
FPNWVKTYIK FLQNSNLGGI IPTVNGKPVP PMLTSPNDFP NWVKTYIKFL QNSNLGGIIP
TVNGKPVRQI TDDELTFLYN TFQIFAPSQF LPTWVKDILS VDYTDIMKIL SKSIEKMQSD
TQEANDIVTL ANLQYNGSTP ADAFETKVTN IIDRLNNNGI HINNKVACQL IMRGLSGEYK
FLRYTRHRHL NMTVAELFLD IHAIYEEQQG SRNSKPNYRR NPSDEKNDSR SYTNTTKPKV
IARNPQKTNN SKSKTARAHN VSTSNNSPST DNDSISKSTT EPIQLNNKHD LHLGQKLTES
TVNHTNHSDD ELPGHLLLDS GASRTLIRSA HHIHSASSNP DINVVDAQKR NIPINAIGDL
QFHFQDNTKT SIKVLHTPNI AYDLLSLNEL AAVDITACFT KNVLERSDGT VLAPIVKYGD
FYWVSKKYLL PSNISVPTIN NVHTSESTRK YPYPFIHRML AHANAQTIRY SLKNNTITYF
NESDVDWSSA IDYQCPDCLI GKSTKHRHIK GSRLKYQNSY EPFQYLHTDI FGPVHNLPKS
APSYFISFTD ETTKFRWVYP LHDRREDSIL DVFTTILAFI KNQFQASVLV IQMDRGSEYT
NRTLHKFLEK NGITPCYTTT ADSRAHGVAE RLNRTLLDDC RTQLQCSGLP NHLWFSAIEF
STIVRNSLAS PKSKKSARQH AGLAGLDIST LLPFGQPVIV NDHNPNSKIH PRGIPGYALH
PSRNSYGYII YLPSLKKTVD TTNYVILQGK ESRLDQFNYD ALTFDEDLNR LTASYHSFIA
SNEIQQSNDL NIESDHDFQS DIELHPEQLR NVLSKAVSPT DSTPPSTHTE DSKRVSKTNI
RAPREVDPNI SESNILPSKK RSSTPQISDI ESTGSGGMHR LDVPLLAPMS QSNTHESSHA
SKSKDFRHSD SYSDNETNHT NVPISSTGGT NNKTVPQTSE QETEKRIIHR SPSIDTSSSE
SNSLHHVVPI KTSDTCPKEN TEESIIADLP LPDLPPEPPT ELSDSFKELP PINSHQTNSS
LGGIGDSNAY TTINSKKRSL EDNETEIKVS RDTWNTKNMR SLEPPRSKKR IHLIAAVKAV
KSIKPIRTTL RYDEAITYNK DIKEKEKYIQ AYHKEVNQLL MMKTWDTDRY YDRKEIDPKR
VINSMFIFNR KRDGTHKARF VARGDIQHPD TYDPGMQSNT VHHYALMTSL SLALDNNYYI
TQLDISSAYL YADIKEELYI RPPPHLGMND KLIRLKKSLY GLKQSGANWY ETIKSYLIKQ
CGMEEVRGWS CVFKNSQVTI CLFVDDMILF SKDLNANKKI ITTLKKQYDT KIINLGESDN
EIQYDILGLE IKYQRGKYMK LGMENSLTEK IPKLNVPLNP KGRKLSAPGQ PGLYIDQDEL
EIDEDEYKEK VHEMQKLIGL ASYVGYKFRF DLLYYINTLA QHILFPSRQV LDMTYELIQF
MWDTRDKQLI WHKNKPTEPD NKLVAISDAS YGNQPYYKSQ IGNIYLLNGK VIGGKSTKAS
LTCTSTTEAE IHAISESVPL LNNLSHLVQE LNKKPITKGL LTDSKSTISI IISNNEEKFR
NRFFGTKAMR LRDEVSGNHL HVCYIETKKN IADVMTKPLP IKTFKLLTNK WIH
