YL22B_YEAST
ID YL22B_YEAST Reviewed; 1598 AA.
AC P0C2J5;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-MAR-2007, sequence version 1.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=Transposon Ty2-LR2 Gag-Pol polyprotein;
DE AltName: Full=TY2A-TY2B;
DE AltName: Full=Transposon Ty2 TYA-TYB polyprotein;
DE Contains:
DE RecName: Full=Capsid protein;
DE Short=CA;
DE Contains:
DE RecName: Full=Ty2 protease;
DE Short=PR;
DE EC=3.4.23.-;
DE Contains:
DE RecName: Full=Integrase;
DE Short=IN;
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;
GN Name=TY2B-LR2; Synonyms=YLRCTy2-2 POL; OrderedLocusNames=YLR424C-A;
GN ORFNames=L9576.6c;
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=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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, AND IDENTIFICATION OF DELETION.
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. 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 Ty2 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.;
CC Name=Transposon Ty2-LR2 Gag-Pol polyprotein;
CC IsoId=P0C2J5-1; Sequence=Displayed;
CC Name=Transposon Ty2-LR2 Gag polyprotein;
CC IsoId=P0C2J6-1; 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, 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. Ty2 retrotransposons belong
CC to the copia elements (pseudoviridae).
CC -!- MISCELLANEOUS: [Isoform Transposon Ty2-LR2 Gag-Pol polyprotein]:
CC Produced by +1 ribosomal frameshifting between codon Leu-431 and Gly-
CC 432 of the TY2A ORF.
CC -!- CAUTION: Could be the product of a pseudogene unlikely to encode a
CC functional protein. Transposon Ty2-DR2 (YLRCTy2-2) contains a 172 aa
CC deletion at position 1540 compared to other Ty2 elements. Because of
CC that it is not part of the S.cerevisiae S288c complete/reference
CC proteome set. {ECO:0000305|PubMed:24374639,
CC ECO:0000305|PubMed:9582191}.
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DR EMBL; U20939; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; S69967; S69967.
DR AlphaFoldDB; P0C2J5; -.
DR MEROPS; A11.003; -.
DR PeptideAtlas; P0C2J5; -.
DR PRIDE; P0C2J5; -.
DR InParanoid; P0C2J5; -.
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; 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; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
PE 5: Uncertain;
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 Ribosomal frameshifting; RNA-binding; RNA-directed DNA polymerase;
KW Transferase; Transposable element; Transposition;
KW Viral release from host cell; Virion maturation; Zinc; Zinc-finger.
FT CHAIN 1..1598
FT /note="Transposon Ty2-LR2 Gag-Pol polyprotein"
FT /id="PRO_0000279332"
FT CHAIN 1..397
FT /note="Capsid protein"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279333"
FT CHAIN 398..578
FT /note="Ty2 protease"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279334"
FT CHAIN 579..1232
FT /note="Integrase"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279335"
FT CHAIN 1233..1598
FT /note="Reverse transcriptase/ribonuclease H"
FT /evidence="ECO:0000250"
FT /id="PRO_0000279336"
FT DOMAIN 656..831
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT DOMAIN 1353..1491
FT /note="Reverse transcriptase Ty1/copia-type"
FT REGION 1..88
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 295..397
FT /note="RNA-binding"
FT /evidence="ECO:0000250"
FT REGION 359..449
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 579..636
FT /note="Integrase-type zinc finger-like"
FT REGION 915..934
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1004..1034
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1059..1135
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1146..1165
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1170..1205
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1193..1227
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 359..440
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1060..1108
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1170..1187
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1188..1205
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 457
FT /note="For protease activity; shared with dimeric partner"
FT /evidence="ECO:0000250"
FT BINDING 667
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 732
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 1361
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 1442
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 1443
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 SITE 397..398
FT /note="Cleavage; by Ty2 protease"
FT /evidence="ECO:0000250"
FT SITE 578..579
FT /note="Cleavage; by Ty2 protease"
FT /evidence="ECO:0000250"
FT SITE 1232..1233
FT /note="Cleavage; by Ty2 protease"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1598 AA; 182564 MW; A802B8AA3036CFF0 CRC64;
MESQQLHQNP HSLHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV NSQEETTPGT
SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN WAHYQQPSMM TCSHYQTSPA
YYQPDPHYPL PQYIPPLSTS SPDPIDSQDQ HSEVPQAKTK VRNNVLPPHT LTSEENFSTW
VKFYIRFLKN SNLGDIIPND QGEIKRQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN
YSDILTVLCK SVSKMQTNNQ ELKDWIALAN LEYNGSTSAD TFEITVSTII QRLKENNINV
SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN LNKPSQYKQH
SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA TSSKFSRVNN DHINESTVSS
QYLSDDNELS LGQQQKESKP TRTIDSNDEL PDHLLIDSGA SQTLVRSAHY LHHATPNSEI
NIVDAQKQDI PINAIGNLHF NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN
TLERSDGTVL APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH
ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS RLKYQESYEP
FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH DRREESILNV FTSILAFIKN
QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG ITACYTTTAD SRAHGVAERL NRTLLNDCRT
LLHCSGLPNH LWFSAVEFST IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN
HNPDSKIHPR GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQNKQT KLDQFDYDTL
TFDDDLNRLT AHNQSFIEQN ETEQSYDQNK ESDHDYQSEI EINSDPLVND FSSQSINPLQ
LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE STEMGGTVES DTTSPRHSST
FTARNQNRPG STNEMIDLTS QDRVNYGLEN IKTTRLGGTE EPYIQRNSDT NIKYRTTNST
PSIDDRSSNS ESTTPIISIE TKAVCDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD
SILDDLPLPD LTHKSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN
ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD EAITYNKDNK
EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN SMFIFNKKRD GTHKARFVAR
SDIQHPDTYD SDMQSNTVHH YALMTSLSIA LDNDYYITQL DISSAYLYAD IKEELYIRPP
PHLGLNDKLL RLRKSLYGLK QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF
VDDMILFSKD LNANKKIITT LKKQYDTKII NLGEGDNEIQ YDILGLEIKY QRSKYMKLGM
EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEIN EEKFRNRFFG TKAMRLRDEV
SGNNLYVYYI ETKKNIADVM TKPLPIKTFK LLTNKWIH
