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P0C2J7

- YH41B_YEAST

UniProt

P0C2J7 - YH41B_YEAST

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Protein
Transposon Ty4-H Gag-Pol polyprotein
Gene
TY4B-H, YHLWTy4-1 POL, YHL009W-B, YHL008W-A
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 sitei414 – 4141For protease activity; shared with dimeric partner By similarity
Metal bindingi630 – 6301Magnesium; catalytic; for integrase activity By similarity
Metal bindingi695 – 6951Magnesium; catalytic; for integrase activity By similarity
Metal bindingi1383 – 13831Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1462 – 14621Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1463 – 14631Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1644 – 16441Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1686 – 16861Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1720 – 17201Magnesium; 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-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: 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 polyprotein
PRO_0000279380Add
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

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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini619 – 786168Integrase catalytic
Add
BLAST
Domaini1375 – 1510136Reverse transcriptase Ty1/copia-type
Add
BLAST
Domaini1644 – 1790147RNase H Ty1/copia-type
Add
BLAST

Region

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

GeneTreeiENSGT00720000109470.
HOGENOMiHOG000155565.
OMAiFERASTY.
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-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

MATPVRDETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVKQ     50
YQRNLNRFKT ILNGLKAEEE KLSETDDIQM LAEKLLKLGE TIDKVENRIV 100
DLVEKIQLLE TNENNNILHE HIDATGTYYL FDTLTSTNKR FYPKDCVFDY 150
RTNNVENIPI LLNNFKKFIK KYQFDDVFEN DIIEIDPREN EILCKIIKEG 200
LGESLDIMNT NTTDIFRIID GLKNKYRSLH GRDVRIRAWE KVLVDTTCRN 250
SALLMNKLQK LVLMEKWIFS KCCQDCPNLK DYLQEAIMGT LHESLRNSVK 300
QRLYNIPHNV GINHEEFLIN TVIETVIDLS PIADDQIENS CMYCKSVFHC 350
SINCKKKPNR ELGLTRPISQ KPIIYKVHRD NNNLSPVQNE QKSWNKTQKK 400
SNKVYNSKKL VIIDTGSGVN ITNDKTLLHN YEDSNRSTRF FGIGKNSSVS 450
VKGYGYIKIK NGHNNTDNKC LLTYYVPEEE STIISCYDLA KKTKMVLSRK 500
YTRLGNKIIK IKTKIVNGVI HVKMNELIER PSDDSKINAI KPTSSPGFKL 550
NKRSITLEDA HKRMGHTGIQ QIENSIKHNH YEESLDLIKE PNEFWCQTCK 600
ISKATKRNHY TGSMNNHSTD HEPGSSWCMD IFGPVSSSNA DTKRYMLIMV 650
DNNTRYCMTS THFNKNAETI LAQIRKNIQY VETQFDRKVR EINSDRGTEF 700
TNDQIEEYFI SKGIHHILTS TQDHAANGRA ERYIRTIVTD ATTLLRQSNL 750
RVKFWEYAVT SATNIRNCLE HKSTGKLPLK AISRQPVTVR LMSFLPFGEK 800
GIIWNHNHKK LKPSGLPSII LCKDPNSYGY KFFIPSKNKI VTSDNYTIPN 850
YTMDGRVRNT QNIYKSHQFS SHNDNEEDQI ETVTNLCEAL ENYEDDNKPI 900
TRLEDLFTEE ELSQIDSNAK YPSPSNNLEG DLDYVFSDVE ESGDYDVESE 950
LSTTNTSIST DKNKILSNKD FNSELASTEI SISEIDKKGL INTSHIDEDK 1000
YDEKVHRIPS IIQEKLVGSK NTIKINDENR ISDRIRSKNI GSILNTGLSR 1050
CVDITDESIT NKDESMHNAK PELIQEQFNK TNHETSFPKE GSIGTNVKFR 1100
NTDNEISLKT GDTSLPIKTL ESINNHHSND YSTNKVEKFE KENHHPPPIE 1150
DIVDMSDQTD MESNCQDGNN LKELKVTDKN VPTDNGTNVS PRLEQNIEAS 1200
GSPVQTVNKS AFLNKEFSSL NMKRKRKRHD KNNSLTSYEL ERDKKRSKRN 1250
RVKLIPDNME TVSAQKIRAI YYNEAISKNP DLKEKHEYKQ AYHKELQNLK 1300
DMKVFDVDVK YSRSEIPDNL IVPTNTIFTK KRNGIYKARI VCRGDTQSPD 1350
TYSVITTESL NHNHIKIFLM IANNRNMFMK TLDINHAFLY AKLEEEIYIP 1400
HPHDRRCVVK LNKALYGLKQ SPKEWNDHLR QYLNGIGLKD NSYTPGLYQT 1450
EDKNLMIAVY VDDCVIAASN EQRLDEFINK LKSNFELKIT GTLIDDVLDT 1500
DILGMDLVYN KRLGTIDLTL KSFINRMDKK YNEELKKIRK SSIPHMSTYK 1550
IDPKKDVLQM SEEEFRQGVL KLQQLLGELN YVRHKCRYDI NFAVKKVARL 1600
VNYPHERVFY MIYKIIQYLV RYKDIGIHYD RDCNKDKKVI AITDASVGSE 1650
YDAQSRIGVI LWYGMNIFNV YSNKSTNRCV SSTEAELHAI YEGYADSETL 1700
KVTLKELGEG DNNDIVMITD SKPAIQGLNR SYQQPKEKFT WIKTEIIKEK 1750
IKEKSIKLLK ITGKGNIADL LTKPVSASDF KRFIQVLKNK ITSQDILAST 1800
DY 1802

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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
U11581 Genomic DNA. No translation available.
BK006934 Genomic DNA. Translation: DAA06678.1 .
PIRi S52611.
RefSeqi NP_058133.1. NM_001184404.1. [P0C2J7-1 ]

3D structure databases

ProteinModelPortali P0C2J7.
ModBasei Search...

Protein-protein interaction databases

BioGridi 36417. 6 interactions.
STRINGi 4932.YHL009W-B.

Proteomic databases

PRIDEi P0C2J7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YHL009W-B ; YHL009W-B ; YHL009W-B . [P0C2J7-1 ]
GeneIDi 856380.
KEGGi sce:YHL009W-B.

Organism-specific databases

SGDi S000007372. YHL009W-B.

Phylogenomic databases

GeneTreei ENSGT00720000109470.
HOGENOMi HOG000155565.
OMAi FERASTY.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 981875.

Gene expression databases

Genevestigatori P0C2J7.

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. 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(1998) [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(2005) [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: July 9, 2014
This is version 64 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