P0C2J7 (YH41B_YEAST) Reviewed, UniProtKB/Swiss-Prot
Last modified November 13, 2013. Version 59. History...
Names and origin
|Protein names||Recommended name:|
Transposon Ty4-H Gag-Pol polyprotein
Transposon Ty4 TYA-TYB polyprotein
|Organism||Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]|
|Taxonomic identifier||559292 [NCBI]|
|Taxonomic lineage||Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›|
|Sequence length||1802 AA.|
|Protein existence||Evidence at transcript level|
General annotation (Comments)
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Endonucleolytic cleavage to 5'-phosphomonoester.
The protease is a homodimer, whose active site consists of two apposed aspartic acid residues By similarity.
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,D35E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.
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.
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).
Contains 1 integrase catalytic domain.
Contains 1 reverse transcriptase Ty1/copia-type domain.
Contains 1 RNase H Ty1/copia-type domain.
|This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]|
Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift.
|Isoform Transposon Ty4-H Gag-Pol polyprotein (identifier: P0C2J7-1) |
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.
|Note: Produced by +1 ribosomal frameshifting between codon Leu-362 and Gly-363 of the YHL009W-A ORF.|
|Isoform Transposon Ty4-H Gag polyprotein (identifier: Q6Q5P6-1) |
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.|
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Chain||1 – 1802||1802||Transposon Ty4-H Gag-Pol polyprotein||PRO_0000279380|
|Domain||619 – 786||168||Integrase catalytic|
|Domain||1375 – 1510||136||Reverse transcriptase Ty1/copia-type|
|Domain||1644 – 1790||147||RNase H Ty1/copia-type|
|Region||381 – 501||121||Ty4 protease|
|Region||539 – 599||61||Integrase-type zinc finger-like|
|Coiled coil||39 – 115||77||Potential|
|Active site||414||1||For protease activity; shared with dimeric partner By similarity|
|Metal binding||630||1||Magnesium; catalytic; for integrase activity By similarity|
|Metal binding||695||1||Magnesium; catalytic; for integrase activity By similarity|
|Metal binding||1383||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1462||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1463||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1644||1||Magnesium; catalytic; for RNase H activity By similarity|
|Metal binding||1686||1||Magnesium; catalytic; for RNase H activity By similarity|
|Metal binding||1720||1||Magnesium; catalytic; for RNase H activity By similarity|
|||"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII."|
Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. Vaudin M.
Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
|||Saccharomyces Genome Database|
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
|||"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.
|||"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.
|+||Additional computationally mapped references.|
|U11581 Genomic DNA. No translation available.|
BK006934 Genomic DNA. Translation: DAA06678.1.
|RefSeq||NP_058133.1. NM_001184404.1. |
3D structure databases
Protein-protein interaction databases
Protocols and materials databases
Genome annotation databases
|EnsemblFungi||YHL009W-B; YHL009W-B; YHL009W-B. |
|SGD||S000007372. YHL009W-B. |
Gene expression databases
Family and domain databases
|InterPro||IPR001584. Integrase_cat-core. |
|Pfam||PF00665. rve. 1 hit. |
PF07727. RVT_2. 1 hit.
|SMART||SM00343. ZnF_C2HC. 1 hit. |
|SUPFAM||SSF53098. SSF53098. 1 hit. |
|PROSITE||PS50994. INTEGRASE. 1 hit. |
|Accession||Primary (citable) accession number: P0C2J7|
Secondary accession number(s): D3DKQ5
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Fungal Protein Annotation Program|