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Transposon Ty2-OR2 Gag-Pol polyprotein (TY2A-TY2B) (Transposon Ty2 TYA-TYB polyprotein) [Cleaved into: Capsid protein (CA); Ty2 protease (PR) (EC 3.4.23.-); Integrase (IN); Reverse transcriptase/ribonuclease H (RT) (RT-RH) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4)]

 YO22B_YEAST             Reviewed;        1770 AA.
Q12501; D6W338;
06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
22-NOV-2017, entry version 126.
RecName: Full=Transposon Ty2-OR2 Gag-Pol polyprotein;
AltName: Full=TY2A-TY2B;
AltName: Full=Transposon Ty2 TYA-TYB polyprotein;
Contains:
RecName: Full=Capsid protein;
Short=CA;
Contains:
RecName: Full=Ty2 protease;
Short=PR;
EC=3.4.23.-;
Contains:
RecName: Full=Integrase;
Short=IN;
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;
Name=TY2B-OR2; Synonyms=YORWTy2-2 POL; OrderedLocusNames=YOR343W-B;
ORFNames=O6304;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169874;
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[2]
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).
[3]
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).
[4]
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).
[5]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
-!- FUNCTION: Capsid protein (CA) is the structural component of the
virus-like particle (VLP), forming the shell that encapsulates the
retrotransposons dimeric RNA genome. The particles are assembled
from trimer-clustered units and there are holes in the capsid
shells that allow for the diffusion of macromolecules. CA has also
nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met
annealing to the multipartite primer-binding site (PBS),
dimerization of Ty2 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).
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester.
-!- SUBUNIT: The capsid protein forms a homotrimer, from which the
VLPs are assembled. The protease is a homodimer, whose active site
consists of two apposed aspartic acid residues (By similarity).
{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 Ty2-OR2 Gag-Pol polyprotein;
IsoId=Q12501-1; Sequence=Displayed;
Note=Produced by +1 ribosomal frameshifting between codon
Leu-431 and Gly-432 of the YOR343W-A ORF.;
Name=Transposon Ty2-OR2 Gag polyprotein;
IsoId=Q12293-1; Sequence=External;
Note=Produced by conventional translation.;
-!- DOMAIN: The C-terminal RNA-binding region of CA is sufficient for
all its nucleocapsid-like chaperone activities. {ECO:0000250}.
-!- 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. Ty2
retrotransposons belong to the copia elements (pseudoviridae).
-!- SEQUENCE CAUTION:
Sequence=DAA11104.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; Z75251; CAA99667.1; -; Genomic_DNA.
EMBL; Z75252; CAA99670.1; -; Genomic_DNA.
EMBL; BK006948; DAA11104.1; ALT_SEQ; Genomic_DNA.
PIR; S70233; S70233.
RefSeq; NP_620389.3; NM_001184390.4.
ProteinModelPortal; Q12501; -.
SMR; Q12501; -.
STRING; 4932.YOR343W-B; -.
MEROPS; A11.003; -.
iPTMnet; Q12501; -.
MaxQB; Q12501; -.
PRIDE; Q12501; -.
GeneID; 854523; -.
KEGG; sce:YOR343W-B; -.
EuPathDB; FungiDB:YOR343W-B; -.
SGD; S000007356; YOR343W-B.
HOGENOM; HOG000280731; -.
InParanoid; Q12501; -.
OrthoDB; EOG092C2F0T; -.
Proteomes; UP000002311; Chromosome XV.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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: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; IPR025724; GAG-pre-integrase_dom.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR021109; Peptidase_aspartic_dom_sf.
InterPro; IPR015820; Retrotransposon_Ty1A_N.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
InterPro; IPR013103; RVT_2.
Pfam; PF13976; gag_pre-integrs; 1.
Pfam; PF00665; rve; 1.
Pfam; PF07727; RVT_2; 1.
Pfam; PF01021; TYA; 1.
SUPFAM; SSF53098; SSF53098; 1.
PROSITE; PS50994; INTEGRASE; 1.
1: Evidence at protein level;
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; Transposition;
Viral release from host cell; Virion maturation; Zinc; Zinc-finger.
CHAIN 1 1770 Transposon Ty2-OR2 Gag-Pol polyprotein.
/FTId=PRO_0000279348.
CHAIN 1 397 Capsid protein. {ECO:0000250}.
/FTId=PRO_0000279349.
CHAIN 398 578 Ty2 protease. {ECO:0000250}.
/FTId=PRO_0000279350.
CHAIN 579 1232 Integrase. {ECO:0000250}.
/FTId=PRO_0000279351.
CHAIN 1233 1770 Reverse transcriptase/ribonuclease H.
{ECO:0000250}.
/FTId=PRO_0000279352.
DOMAIN 656 831 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
DOMAIN 1353 1491 Reverse transcriptase Ty1/copia-type.
DOMAIN 1625 1767 RNase H Ty1/copia-type.
REGION 295 397 RNA-binding. {ECO:0000250}.
REGION 579 636 Integrase-type zinc finger-like.
MOTIF 1193 1227 Bipartite nuclear localization signal.
{ECO:0000250}.
ACT_SITE 457 457 For protease activity; shared with
dimeric partner. {ECO:0000250}.
METAL 667 667 Magnesium; catalytic; for integrase
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 732 732 Magnesium; catalytic; for integrase
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1361 1361 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1442 1442 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1443 1443 Magnesium; catalytic; for reverse
transcriptase activity.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
METAL 1625 1625 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1667 1667 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
METAL 1700 1700 Magnesium; catalytic; for RNase H
activity. {ECO:0000255|PROSITE-
ProRule:PRU00457}.
SITE 397 398 Cleavage; by Ty2 protease. {ECO:0000250}.
SITE 578 579 Cleavage; by Ty2 protease. {ECO:0000250}.
SITE 1232 1233 Cleavage; by Ty2 protease. {ECO:0000250}.
SEQUENCE 1770 AA; 202131 MW; 7E22DF04A753FD49 CRC64;
MESQQLHQNP HCPHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV NSQEETTPGT
SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN WAHYQQPSMM TCSHYQTSPA
YYQPDPHYPL PQYIPPLSTS SPDPIDSQDQ HSEVPQAKTK VRNNVLPPHP HTSEENFSTW
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 DLLSLSELTN 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 NYVILQNNQT KLDQFDYDTL
TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND FSSQSLNPLQ
LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE STEMGGTIES DTTSPRHSST
FTARNQKRPG SPNDMIDLTS QDRVNYGLEN IKTTRLGGTE EPYIQRNSDT NIKYRTTNST
PSIDDRSSNS DSTTPIISIE TKAACDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD
SILDDLPLPD LTHKSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN
ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD EAITYNKDNK
EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN SMFIFNKKRD GTHKARFVAR
GDIQHPDTYD SDMQSNTVHH YALMTSLSIA LDNDYYITQL DISSAYLYAD IKEELYIRPP
PHLGLNDKLL RLRKSLYGLK QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF
VDDMILFSKD LNANKKIITT LKKQYDTKII NLGEGDNEIQ YDILGLEIKY QRSKYMKLGM
EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE MQKLIGLASY
VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD TRDKQLIWHK NKPTKPDNKL
VAISDASYGN QPYYKSQIGN IFLLNGKVIG GKSTKASLTC TSTTEAEIHA VSEAIPLLNN
LSHLVQELNK KPIIKGLLTD SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY
YIETKKNIAD VMTKPLPIKT FKLLTNKWIH


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