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P47024

- YJ41B_YEAST

UniProt

P47024 - YJ41B_YEAST

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Protein

Transposon Ty4-J Gag-Pol polyprotein

Gene

TY4B-J

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi

Functioni

Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome.By similarity
The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.By similarity
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).By similarity
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).By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Endonucleolytic cleavage to 5'-phosphomonoester.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei415 – 4151For protease activity; shared with dimeric partnerBy similarity
Metal bindingi631 – 6311Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Metal bindingi696 – 6961Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Metal bindingi1384 – 13841Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1463 – 14631Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1464 – 14641Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1645 – 16451Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1687 – 16871Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1721 – 17211Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. ATP binding Source: UniProtKB-KW
  3. DNA binding Source: UniProtKB-KW
  4. DNA-directed DNA polymerase activity Source: SGD
  5. peptidase activity Source: SGD
  6. ribonuclease activity Source: SGD
  7. RNA binding Source: SGD
  8. RNA-directed DNA polymerase activity Source: SGD
  9. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC
  10. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA-dependent DNA replication Source: GOC
  2. DNA integration Source: UniProtKB-KW
  3. DNA recombination Source: UniProtKB-KW
  4. RNA-dependent DNA replication Source: GOC
  5. RNA phosphodiester bond hydrolysis Source: GOC
  6. transposition, RNA-mediated Source: SGD
  7. viral release from host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Transposition, Virion maturation, Virus exit from host cell

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Transposon Ty4-J Gag-Pol polyprotein
Alternative name(s):
TY4A-TY4B
Transposon Ty4 TYA-TYB polyprotein
Including the following 4 domains:
Capsid protein
Short name:
CA
Ty4 protease (EC:3.4.23.-)
Short name:
PR
Integrase
Short name:
IN
Reverse transcriptase/ribonuclease H (EC:2.7.7.49, EC:2.7.7.7, EC:3.1.26.4)
Short name:
RT
Short name:
RT-RH
Gene namesi
Name:TY4B-J
Synonyms:YJLWTy4-1 POL
Ordered Locus Names:YJL113W
ORF Names:J0780
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome X

Organism-specific databases

SGDiS000003649. YJL113W.

Subcellular locationi

Cytoplasm. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. nucleus Source: SGD
  3. retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 18031803Transposon Ty4-J Gag-Pol polyproteinPRO_0000203502Add
BLAST

Post-translational modificationi

Proteolytically processed into capsid protein (CA), Ty4 protease (PR), integrase (IN) and reverse transcriptase/ribonuclease H (RT) proteins (Probable). 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).By similarityCurated

Proteomic databases

PaxDbiP47024.

Expressioni

Gene expression databases

GenevestigatoriP47024.

Interactioni

Subunit structurei

The protease is a homodimer, whose active site consists of two apposed aspartic acid residues.By similarity

Protein-protein interaction databases

BioGridi33642. 19 interactions.
IntActiP47024. 6 interactions.
MINTiMINT-436711.
STRINGi4932.YJL113W.

Structurei

3D structure databases

ProteinModelPortaliP47024.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini620 – 787168Integrase catalyticPROSITE-ProRule annotationAdd
BLAST
Domaini1376 – 1511136Reverse transcriptase Ty1/copia-typeAdd
BLAST
Domaini1645 – 1791147RNase H Ty1/copia-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni382 – 502121Ty4 proteaseAdd
BLAST
Regioni540 – 60061Integrase-type zinc finger-likeAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili39 – 11577Sequence AnalysisAdd
BLAST

Domaini

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).By similarity

Sequence similaritiesi

Contains 1 integrase catalytic domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiNOG283194.
HOGENOMiHOG000155565.
InParanoidiP47024.
OrthoDBiEOG7TJ3S3.

Family and domain databases

Gene3Di3.30.420.10. 2 hits.
InterProiIPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50994. INTEGRASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift.

Isoform Transposon Ty4-J Gag-Pol polyprotein (identifier: P47024-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MATPVRGETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVRQ
60 70 80 90 100
YQRNLNRFKT ILNGLKAEEE KLSEADDIQM LAEKLLKLGE TIDKVENRIV
110 120 130 140 150
DLVEKIQLLE TNENNNILHE HIDATGTYYL FDTLTSTNKR FYPKDCVFDY
160 170 180 190 200
RTNNVENIPI LLNNFKKFIK KYQFDDVFEN DIIEIDPREN EILCKIIKEG
210 220 230 240 250
LGESLDIMNT NTTDIFRIID GLKKQNIEVC MVEMSELEPG EKVLVDTTCR
260 270 280 290 300
NSALLMNKLQ KLVLMEKWIF SKCCQDCPNL KDYLQEAIMG TLHESLRNSV
310 320 330 340 350
KQRLYNIPHD VGIDHEEFLI NTVIETVIDL SPIADDQIEN SCMYCKSVFH
360 370 380 390 400
CSINCKKKPN RELGLTRPIS QKPIIYKVHR DNNHLSPVQN EQKSWNKTQK
410 420 430 440 450
RSNKVYNSKK LVIIDTGSGV NITNDKTLLH NYEDSNRSTR FFGIGKNSSV
460 470 480 490 500
SVKGYGYIKI KNGHNNTDNK CLLTYYVPEE ESTIISCYDL AKKTKMVLSR
510 520 530 540 550
KYTRLGNKII KIKTKIVNGV IHVKMNELIE RPSDDSKINA IKPTSSPGFK
560 570 580 590 600
LNKRSITLED AHKRMGHTGI QQIENSIKHN HYEESLDLIK EPNEFWCQTC
610 620 630 640 650
KISKATKRNH YTGSMNNHST DHEPGSSWCM DIFGPVSSSN ADTKRYMLIM
660 670 680 690 700
VDNNTRYCMT STHFNKNAET ILAQVRKNIQ YVETQFDRKV REINSDRGTE
710 720 730 740 750
FTNDQIEEYF ISKGIHHILT STQDHAANGR AERYIRTIIT DATTLLRQSN
760 770 780 790 800
LRVKFWEYAV TSATNIRNYL EHKSTGKLPL KAISRQPVTV RLMSFLPFGE
810 820 830 840 850
KGIIWNHNHK KLKPSGLPSI ILCKDPNSYG YKFFIPSKNK IVTSDNYTIP
860 870 880 890 900
NYTMDGRVRN TQNINKSHQF SSDNDDEEDQ IETVTNLCEA LENYEDDNKP
910 920 930 940 950
ITRLEDLFTE EELSQIDSNA KYPSPSNNLE GDLDYVFSDV EESGDYDVES
960 970 980 990 1000
ELSTTNNSIS TDKNKILSNK DFNSELASTE ISISGIDKKG LINTSHIDED
1010 1020 1030 1040 1050
KYDEKVHRIP SIIQEKLVGS KNTIKINDEN KISDRIRSKN IGSILNTGLS
1060 1070 1080 1090 1100
RCVDITDESI TNKDESMHNA KPELIQEQLK KTNHETSFPK EGSIGTNVKF
1110 1120 1130 1140 1150
RNTNNEISLK TGDTSLPIKT LESINNHHSN DYSTNKVEKF EKENHHPPPI
1160 1170 1180 1190 1200
EDIVDMSDQT DMESNCQDGN NLKELKVTDK NVPTDNGTNV SPRLEQNIEA
1210 1220 1230 1240 1250
SGSPVQTVNK SAFLNKEFSS LNMKRKRKRH DKNNSLTSYE LERDKKRSKK
1260 1270 1280 1290 1300
NRVKLIPDNM ETVSAPKIRA IYYNEAISKN PDLKEKHEYK QAYHKELQNL
1310 1320 1330 1340 1350
KDMKVFDVDV KYSRSEIPDN LIVPTNTIFT KKRNGIYKAR IVCRGDTQSP
1360 1370 1380 1390 1400
DTYSVITTES LNHNHIKIFL MIANNRNMFM KTLDINHAFL YAKLEEEIYI
1410 1420 1430 1440 1450
PHPHDRRCVV KLNKALYGLK QSPKEWNDHL RQYLNGIGLK DNSYTPGLYQ
1460 1470 1480 1490 1500
TEDKNLMIAV YVDDCVIAAS NEQRLDEFIN KLKSNFELKI TGTLIDDVLD
1510 1520 1530 1540 1550
TDILGMDLVY NKRLGTIDLT LKSFINRMDK KYNEELKKIR KSSIPHMSTY
1560 1570 1580 1590 1600
KIDPKKDVLQ MSEEEFRQGV LKLQQLLGEL NYVRHKCRYD IEFAVKKVAR
1610 1620 1630 1640 1650
LVNYPHERVF YMIYKIIQYL VRYKDIGIHY DRDCNKDKKV IAITDASVGS
1660 1670 1680 1690 1700
EYDAQSRIGV ILWYGMNIFN VYSNKSTNRC VSSTEAELHA IYEGYADSET
1710 1720 1730 1740 1750
LKVTLKELGE GDNNDIVMIT DSKPAIQGLN RSYQQPKEKF TWIKTEIIKE
1760 1770 1780 1790 1800
KIKEKSIKLL KITGKGNIAD LLTKPVSASD FKRFIQVLKN KITSQDILAS

TDY

Note: Produced by +1 ribosomal frameshifting between codon Leu-363 and Gly-364 of the YJL114W ORF.

Length:1,803
Mass (Da):207,710
Last modified:November 2, 2010 - v3
Checksum:iA58D1D4E96F7C9C9
GO
Isoform Transposon Ty4-J Gag polyprotein (identifier: P47023-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry P47023.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:414
Mass (Da):48,035
GO

Sequence cautioni

The sequence DAA08686.2 differs from that shown. Reason: Frameshift at positions 226 and 240.
The sequence CAA89409.1 differs from that shown. Reason: Erroneous gene model prediction.

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti452 – 4521V → L in X67284. (PubMed:1328182)Curated
Sequence conflicti684 – 6841T → A in X67284. (PubMed:1328182)Curated
Sequence conflicti920 – 9201A → S in X67284. (PubMed:1328182)Curated
Sequence conflicti1020 – 10201S → R in X67284. (PubMed:1328182)Curated
Sequence conflicti1803 – 18031Y → YLINEVLNTQISVEVQ in X67284. (PubMed:1328182)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X67284 Genomic DNA. No translation available.
Z49389 Genomic DNA. Translation: CAA89409.1. Sequence problems.
BK006943 Genomic DNA. Translation: DAA08686.2. Frameshift.
PIRiS31262.
S56894.
RefSeqiNP_012421.2. NM_001181546.2.

Genome annotation databases

GeneIDi853330.
KEGGisce:YJL113W.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X67284 Genomic DNA. No translation available.
Z49389 Genomic DNA. Translation: CAA89409.1 . Sequence problems.
BK006943 Genomic DNA. Translation: DAA08686.2 . Frameshift.
PIRi S31262.
S56894.
RefSeqi NP_012421.2. NM_001181546.2.

3D structure databases

ProteinModelPortali P47024.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33642. 19 interactions.
IntActi P47024. 6 interactions.
MINTi MINT-436711.
STRINGi 4932.YJL113W.

Proteomic databases

PaxDbi P47024.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 853330.
KEGGi sce:YJL113W.

Organism-specific databases

SGDi S000003649. YJL113W.

Phylogenomic databases

eggNOGi NOG283194.
HOGENOMi HOG000155565.
InParanoidi P47024.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 973695.

Gene expression databases

Genevestigatori P47024.

Family and domain databases

Gene3Di 3.30.420.10. 2 hits.
InterProi IPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
IPR001878. Znf_CCHC.
[Graphical view ]
Pfami PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
[Graphical view ]
SMARTi SM00343. ZnF_C2HC. 1 hit.
[Graphical view ]
SUPFAMi SSF53098. SSF53098. 1 hit.
PROSITEi PS50994. INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Ty4, a new retrotransposon from Saccharomyces cerevisiae, flanked by tau-elements."
    Janetzky B., Lehle L.
    J. Biol. Chem. 267:19798-19805(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon."
    Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C.
    Yeast 12:1471-1474(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 226 AND 240.
    Strain: ATCC 204508 / S288c.
  5. "Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence."
    Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.
    Genome Res. 8:464-478(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  6. "Happy together: the life and times of Ty retrotransposons and their hosts."
    Lesage P., Todeschini A.L.
    Cytogenet. Genome Res. 110:70-90(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiYJ41B_YEAST
AccessioniPrimary (citable) accession number: P47024
Secondary accession number(s): D6VW70, P87192
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: November 2, 2010
Last modified: October 29, 2014
This is version 96 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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. Ty4 retrotransposons belong to the copia elements (pseudoviridae).

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

External Data

Dasty 3