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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: 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)DescriptionActionsGraphical viewLength
Active sitei415For protease activity; shared with dimeric partnerBy similarity1
Metal bindingi631Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi696Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1384Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1463Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1464Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1645Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1687Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1721Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1

GO - Molecular functioni

  • aspartic-type endopeptidase activity Source: UniProtKB-KW
  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • peptidase activity Source: SGD
  • ribonuclease activity Source: SGD
  • RNA binding Source: SGD
  • RNA-directed DNA polymerase activity Source: SGD
  • RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

GO - Biological processi

  • DNA integration Source: UniProtKB-KW
  • DNA recombination Source: UniProtKB-KW
  • transposition, RNA-mediated Source: SGD
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
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJL113W.
SGDiS000003649. YJL113W.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
  • retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002035021 – 1803Transposon Ty4-J Gag-Pol polyproteinAdd BLAST1803

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

PRIDEiP47024.

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 interactors.
IntActiP47024. 6 interactors.
MINTiMINT-436711.

Structurei

3D structure databases

ProteinModelPortaliP47024.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini620 – 787Integrase catalyticPROSITE-ProRule annotationAdd BLAST168
Domaini1376 – 1511Reverse transcriptase Ty1/copia-typeAdd BLAST136
Domaini1645 – 1791RNase H Ty1/copia-typeAdd BLAST147

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni382 – 502Ty4 proteaseAdd BLAST121
Regioni540 – 600Integrase-type zinc finger-likeAdd BLAST61

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili39 – 115Sequence analysisAdd BLAST77

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

HOGENOMiHOG000155565.
InParanoidiP47024.
OrthoDBiEOG092C2F0T.

Family and domain databases

Gene3Di3.30.420.10. 2 hits.
InterProiIPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamiPF00665. rve. 1 hit.
PF07727. RVT_2. 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. AlignAdd to basket

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti452V → L in X67284 (PubMed:1328182).Curated1
Sequence conflicti684T → A in X67284 (PubMed:1328182).Curated1
Sequence conflicti920A → S in X67284 (PubMed:1328182).Curated1
Sequence conflicti1020S → R in X67284 (PubMed:1328182).Curated1
Sequence conflicti1803Y → YLINEVLNTQISVEVQ in X67284 (PubMed:1328182).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001181546.3.

Genome annotation databases

GeneIDi853330.
KEGGisce:YJL113W.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001181546.3.

3D structure databases

ProteinModelPortaliP47024.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33642. 19 interactors.
IntActiP47024. 6 interactors.
MINTiMINT-436711.

Proteomic databases

PRIDEiP47024.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi853330.
KEGGisce:YJL113W.

Organism-specific databases

EuPathDBiFungiDB:YJL113W.
SGDiS000003649. YJL113W.

Phylogenomic databases

HOGENOMiHOG000155565.
InParanoidiP47024.
OrthoDBiEOG092C2F0T.

Family and domain databases

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

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: November 30, 2016
This is version 109 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.