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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, YJLWTy4-1 POL, YJL113W, J0780
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.
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.

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 partner By similarity
Metal bindingi631 – 6311Magnesium; catalytic; for integrase activity By similarity
Metal bindingi696 – 6961Magnesium; catalytic; for integrase activity By similarity
Metal bindingi1384 – 13841Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1463 – 14631Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1464 – 14641Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1645 – 16451Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1687 – 16871Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1721 – 17211Magnesium; catalytic; for RNase H activity By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. DNA integration Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. DNA-dependent DNA replication Source: GOC
  4. RNA phosphodiester bond hydrolysis Source: GOC
  5. RNA-dependent DNA replication 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-SubCell
  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 polyprotein
PRO_0000203502Add
BLAST

Post-translational modificationi

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

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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini620 – 787168Integrase catalytic
Add
BLAST
Domaini1376 – 1511136Reverse transcriptase Ty1/copia-type
Add
BLAST
Domaini1645 – 1791147RNase H Ty1/copia-type
Add
BLAST

Region

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

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili39 – 11577 Reviewed prediction
Add
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.

Sequence similaritiesi

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiNOG283194.
HOGENOMiHOG000155565.
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

MATPVRGETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVRQ     50
YQRNLNRFKT ILNGLKAEEE KLSEADDIQM LAEKLLKLGE TIDKVENRIV 100
DLVEKIQLLE TNENNNILHE HIDATGTYYL FDTLTSTNKR FYPKDCVFDY 150
RTNNVENIPI LLNNFKKFIK KYQFDDVFEN DIIEIDPREN EILCKIIKEG 200
LGESLDIMNT NTTDIFRIID GLKKQNIEVC MVEMSELEPG EKVLVDTTCR 250
NSALLMNKLQ KLVLMEKWIF SKCCQDCPNL KDYLQEAIMG TLHESLRNSV 300
KQRLYNIPHD VGIDHEEFLI NTVIETVIDL SPIADDQIEN SCMYCKSVFH 350
CSINCKKKPN RELGLTRPIS QKPIIYKVHR DNNHLSPVQN EQKSWNKTQK 400
RSNKVYNSKK LVIIDTGSGV NITNDKTLLH NYEDSNRSTR FFGIGKNSSV 450
SVKGYGYIKI KNGHNNTDNK CLLTYYVPEE ESTIISCYDL AKKTKMVLSR 500
KYTRLGNKII KIKTKIVNGV IHVKMNELIE RPSDDSKINA IKPTSSPGFK 550
LNKRSITLED AHKRMGHTGI QQIENSIKHN HYEESLDLIK EPNEFWCQTC 600
KISKATKRNH YTGSMNNHST DHEPGSSWCM DIFGPVSSSN ADTKRYMLIM 650
VDNNTRYCMT STHFNKNAET ILAQVRKNIQ YVETQFDRKV REINSDRGTE 700
FTNDQIEEYF ISKGIHHILT STQDHAANGR AERYIRTIIT DATTLLRQSN 750
LRVKFWEYAV TSATNIRNYL EHKSTGKLPL KAISRQPVTV RLMSFLPFGE 800
KGIIWNHNHK KLKPSGLPSI ILCKDPNSYG YKFFIPSKNK IVTSDNYTIP 850
NYTMDGRVRN TQNINKSHQF SSDNDDEEDQ IETVTNLCEA LENYEDDNKP 900
ITRLEDLFTE EELSQIDSNA KYPSPSNNLE GDLDYVFSDV EESGDYDVES 950
ELSTTNNSIS TDKNKILSNK DFNSELASTE ISISGIDKKG LINTSHIDED 1000
KYDEKVHRIP SIIQEKLVGS KNTIKINDEN KISDRIRSKN IGSILNTGLS 1050
RCVDITDESI TNKDESMHNA KPELIQEQLK KTNHETSFPK EGSIGTNVKF 1100
RNTNNEISLK TGDTSLPIKT LESINNHHSN DYSTNKVEKF EKENHHPPPI 1150
EDIVDMSDQT DMESNCQDGN NLKELKVTDK NVPTDNGTNV SPRLEQNIEA 1200
SGSPVQTVNK SAFLNKEFSS LNMKRKRKRH DKNNSLTSYE LERDKKRSKK 1250
NRVKLIPDNM ETVSAPKIRA IYYNEAISKN PDLKEKHEYK QAYHKELQNL 1300
KDMKVFDVDV KYSRSEIPDN LIVPTNTIFT KKRNGIYKAR IVCRGDTQSP 1350
DTYSVITTES LNHNHIKIFL MIANNRNMFM KTLDINHAFL YAKLEEEIYI 1400
PHPHDRRCVV KLNKALYGLK QSPKEWNDHL RQYLNGIGLK DNSYTPGLYQ 1450
TEDKNLMIAV YVDDCVIAAS NEQRLDEFIN KLKSNFELKI TGTLIDDVLD 1500
TDILGMDLVY NKRLGTIDLT LKSFINRMDK KYNEELKKIR KSSIPHMSTY 1550
KIDPKKDVLQ MSEEEFRQGV LKLQQLLGEL NYVRHKCRYD IEFAVKKVAR 1600
LVNYPHERVF YMIYKIIQYL VRYKDIGIHY DRDCNKDKKV IAITDASVGS 1650
EYDAQSRIGV ILWYGMNIFN VYSNKSTNRC VSSTEAELHA IYEGYADSET 1700
LKVTLKELGE GDNNDIVMIT DSKPAIQGLN RSYQQPKEKF TWIKTEIIKE 1750
KIKEKSIKLL KITGKGNIAD LLTKPVSASD FKRFIQVLKN KITSQDILAS 1800
TDY 1803

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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti452 – 4521V → L in X67284. 1 Publication
Sequence conflicti684 – 6841T → A in X67284. 1 Publication
Sequence conflicti920 – 9201A → S in X67284. 1 Publication
Sequence conflicti1020 – 10201S → R in X67284. 1 Publication
Sequence conflicti1803 – 18031Y → YLINEVLNTQISVEVQ in X67284. 1 Publication

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...

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.
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: June 11, 2014
This is version 94 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

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