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Protein

Transposon Ty4-H Gag-Pol polyprotein

Gene

TY4B-H

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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei414 – 4141For protease activity; shared with dimeric partnerBy similarity
Metal bindingi630 – 6301Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Metal bindingi695 – 6951Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Metal bindingi1383 – 13831Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1462 – 14621Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1463 – 14631Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1644 – 16441Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1686 – 16861Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1720 – 17201Magnesium; 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 biosynthetic process 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-H 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-H
Synonyms:YHLWTy4-1 POL
Ordered Locus Names:YHL009W-B
ORF Names:YHL008W-A
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome VIII

Organism-specific databases

SGDiS000007372. YHL009W-B.

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 – 18021802Transposon Ty4-H Gag-Pol polyproteinPRO_0000279380Add
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

PRIDEiP0C2J7.

Expressioni

Gene expression databases

GenevestigatoriP0C2J7.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi36417. 6 interactions.
STRINGi4932.YHL009W-B.

Structurei

3D structure databases

ProteinModelPortaliP0C2J7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini619 – 786168Integrase catalyticPROSITE-ProRule annotationAdd
BLAST
Domaini1375 – 1510136Reverse transcriptase Ty1/copia-typeAdd
BLAST
Domaini1644 – 1790147RNase H Ty1/copia-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni381 – 501121Ty4 proteaseAdd
BLAST
Regioni539 – 59961Integrase-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

GeneTreeiENSGT00720000109470.
HOGENOMiHOG000155565.
InParanoidiP0C2J7.
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. AlignAdd to basket

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

Isoform Transposon Ty4-H Gag-Pol polyprotein (identifier: P0C2J7-1) [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
MATPVRDETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVKQ
60 70 80 90 100
YQRNLNRFKT ILNGLKAEEE KLSETDDIQM 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 GLKNKYRSLH GRDVRIRAWE KVLVDTTCRN
260 270 280 290 300
SALLMNKLQK LVLMEKWIFS KCCQDCPNLK DYLQEAIMGT LHESLRNSVK
310 320 330 340 350
QRLYNIPHNV GINHEEFLIN TVIETVIDLS PIADDQIENS CMYCKSVFHC
360 370 380 390 400
SINCKKKPNR ELGLTRPISQ KPIIYKVHRD NNNLSPVQNE QKSWNKTQKK
410 420 430 440 450
SNKVYNSKKL VIIDTGSGVN ITNDKTLLHN YEDSNRSTRF FGIGKNSSVS
460 470 480 490 500
VKGYGYIKIK NGHNNTDNKC LLTYYVPEEE STIISCYDLA KKTKMVLSRK
510 520 530 540 550
YTRLGNKIIK IKTKIVNGVI HVKMNELIER PSDDSKINAI KPTSSPGFKL
560 570 580 590 600
NKRSITLEDA HKRMGHTGIQ QIENSIKHNH YEESLDLIKE PNEFWCQTCK
610 620 630 640 650
ISKATKRNHY TGSMNNHSTD HEPGSSWCMD IFGPVSSSNA DTKRYMLIMV
660 670 680 690 700
DNNTRYCMTS THFNKNAETI LAQIRKNIQY VETQFDRKVR EINSDRGTEF
710 720 730 740 750
TNDQIEEYFI SKGIHHILTS TQDHAANGRA ERYIRTIVTD ATTLLRQSNL
760 770 780 790 800
RVKFWEYAVT SATNIRNCLE HKSTGKLPLK AISRQPVTVR LMSFLPFGEK
810 820 830 840 850
GIIWNHNHKK LKPSGLPSII LCKDPNSYGY KFFIPSKNKI VTSDNYTIPN
860 870 880 890 900
YTMDGRVRNT QNIYKSHQFS SHNDNEEDQI ETVTNLCEAL ENYEDDNKPI
910 920 930 940 950
TRLEDLFTEE ELSQIDSNAK YPSPSNNLEG DLDYVFSDVE ESGDYDVESE
960 970 980 990 1000
LSTTNTSIST DKNKILSNKD FNSELASTEI SISEIDKKGL INTSHIDEDK
1010 1020 1030 1040 1050
YDEKVHRIPS IIQEKLVGSK NTIKINDENR ISDRIRSKNI GSILNTGLSR
1060 1070 1080 1090 1100
CVDITDESIT NKDESMHNAK PELIQEQFNK TNHETSFPKE GSIGTNVKFR
1110 1120 1130 1140 1150
NTDNEISLKT GDTSLPIKTL ESINNHHSND YSTNKVEKFE KENHHPPPIE
1160 1170 1180 1190 1200
DIVDMSDQTD MESNCQDGNN LKELKVTDKN VPTDNGTNVS PRLEQNIEAS
1210 1220 1230 1240 1250
GSPVQTVNKS AFLNKEFSSL NMKRKRKRHD KNNSLTSYEL ERDKKRSKRN
1260 1270 1280 1290 1300
RVKLIPDNME TVSAQKIRAI YYNEAISKNP DLKEKHEYKQ AYHKELQNLK
1310 1320 1330 1340 1350
DMKVFDVDVK YSRSEIPDNL IVPTNTIFTK KRNGIYKARI VCRGDTQSPD
1360 1370 1380 1390 1400
TYSVITTESL NHNHIKIFLM IANNRNMFMK TLDINHAFLY AKLEEEIYIP
1410 1420 1430 1440 1450
HPHDRRCVVK LNKALYGLKQ SPKEWNDHLR QYLNGIGLKD NSYTPGLYQT
1460 1470 1480 1490 1500
EDKNLMIAVY VDDCVIAASN EQRLDEFINK LKSNFELKIT GTLIDDVLDT
1510 1520 1530 1540 1550
DILGMDLVYN KRLGTIDLTL KSFINRMDKK YNEELKKIRK SSIPHMSTYK
1560 1570 1580 1590 1600
IDPKKDVLQM SEEEFRQGVL KLQQLLGELN YVRHKCRYDI NFAVKKVARL
1610 1620 1630 1640 1650
VNYPHERVFY MIYKIIQYLV RYKDIGIHYD RDCNKDKKVI AITDASVGSE
1660 1670 1680 1690 1700
YDAQSRIGVI LWYGMNIFNV YSNKSTNRCV SSTEAELHAI YEGYADSETL
1710 1720 1730 1740 1750
KVTLKELGEG DNNDIVMITD SKPAIQGLNR SYQQPKEKFT WIKTEIIKEK
1760 1770 1780 1790 1800
IKEKSIKLLK ITGKGNIADL LTKPVSASDF KRFIQVLKNK ITSQDILAST

DY

Note: Produced by +1 ribosomal frameshifting between codon Leu-362 and Gly-363 of the YHL009W-A ORF.

Length:1,802
Mass (Da):207,970
Last modified:March 6, 2007 - v1
Checksum:i7F6A8A3483966588
GO
Isoform Transposon Ty4-H Gag polyprotein (identifier: Q6Q5P6-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry Q6Q5P6.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:413
Mass (Da):48,214
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U11581 Genomic DNA. No translation available.
BK006934 Genomic DNA. Translation: DAA06678.1.
PIRiS52611.
RefSeqiNP_058133.1. NM_001184404.1. [P0C2J7-1]

Genome annotation databases

EnsemblFungiiYHL009W-B; YHL009W-B; YHL009W-B. [P0C2J7-1]
GeneIDi856380.
KEGGisce:YHL009W-B.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U11581 Genomic DNA. No translation available.
BK006934 Genomic DNA. Translation: DAA06678.1.
PIRiS52611.
RefSeqiNP_058133.1. NM_001184404.1. [P0C2J7-1]

3D structure databases

ProteinModelPortaliP0C2J7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36417. 6 interactions.
STRINGi4932.YHL009W-B.

Proteomic databases

PRIDEiP0C2J7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYHL009W-B; YHL009W-B; YHL009W-B. [P0C2J7-1]
GeneIDi856380.
KEGGisce:YHL009W-B.

Organism-specific databases

SGDiS000007372. YHL009W-B.

Phylogenomic databases

GeneTreeiENSGT00720000109470.
HOGENOMiHOG000155565.
InParanoidiP0C2J7.
OrthoDBiEOG7TJ3S3.

Miscellaneous databases

NextBioi981875.

Gene expression databases

GenevestigatoriP0C2J7.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "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(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  4. "Happy together: the life and times of Ty retrotransposons and their hosts."
    Lesage P., Todeschini A.L.
    Cytogenet. Genome Res. 110:70-90(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiYH41B_YEAST
AccessioniPrimary (citable) accession number: P0C2J7
Secondary accession number(s): D3DKQ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 6, 2007
Last modified: January 7, 2015
This is version 67 of the entry and version 1 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 VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

External Data

Dasty 3

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 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.