Q04711 (YM11B_YEAST) Reviewed, UniProtKB/Swiss-Prot
Last modified February 19, 2014. Version 105. History...
Names and origin
|Protein names||Recommended name:|
Transposon Ty1-ML1 Gag-Pol polyprotein
Transposon Ty1 TYA-TYB polyprotein
Cleaved into the following 4 chains:
|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||1755 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Inferred from homology|
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. The particles are assembled from trimer-clustered units and there are holes in the capsid shells that allow for the diffusion of macromolecules. CA has also nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty1 RNA and initiation of reverse transcription 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 capsid protein forms a homotrimer, from which the VLPs are assembled. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues By similarity.
The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities By similarity. Ref.5
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. Ref.5
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 yielding capsid protein p45 and a Pol-p154 precursor protein. This cleavage is a prerequisite for subsequent processing of Pol-p154 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. Ty1 retrotransposons belong to the copia elements (pseudoviridae).
Contains 1 integrase catalytic domain.
Contains 1 peptidase A11 domain.
Contains 1 reverse transcriptase Ty1/copia-type domain.
Contains 1 RNase H Ty1/copia-type domain.
The sequence CAA87830.1 differs from that shown. Reason: Erroneous gene model prediction.
|This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]|
Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift. The ratio of Gag:Gag-Pol varies between 20:1 and 5:1 (By similarity).
|Isoform Transposon Ty1-ML1 Gag-Pol polyprotein (identifier: Q04711-1) |
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-435 and Gly-436 of the YML045W-A ORF.|
|Isoform Transposon Ty1-ML1 Gag polyprotein (identifier: Q04706-1) |
The sequence of this isoform can be found in the external entry Q04706.
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 – 1755||1755||Transposon Ty1-ML1 Gag-Pol polyprotein||PRO_0000199566|
|Chain||1 – 401||401||Capsid protein By similarity||PRO_0000279117|
|Chain||402 – 582||181||Ty1 protease By similarity||PRO_0000279118|
|Chain||583 – 1217||635||Integrase By similarity||PRO_0000279119|
|Chain||1218 – 1755||538||Reverse transcriptase/ribonuclease H By similarity||PRO_0000279120|
|Domain||660 – 835||176||Integrase catalytic|
|Domain||1338 – 1476||139||Reverse transcriptase Ty1/copia-type|
|Domain||1610 – 1752||143||RNase H Ty1/copia-type|
|Region||299 – 401||103||RNA-binding By similarity|
|Region||583 – 640||58||Integrase-type zinc finger-like|
|Motif||1178 – 1212||35||Bipartite nuclear localization signal By similarity|
|Compositional bias||72 – 146||75||Pro-rich|
|Active site||461||1||For protease activity; shared with dimeric partner By similarity|
|Metal binding||671||1||Magnesium; catalytic; for integrase activity By similarity|
|Metal binding||736||1||Magnesium; catalytic; for integrase activity By similarity|
|Metal binding||1346||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1427||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1428||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1610||1||Magnesium; catalytic; for RNase H activity By similarity|
|Metal binding||1652||1||Magnesium; catalytic; for RNase H activity By similarity|
|Metal binding||1685||1||Magnesium; catalytic; for RNase H activity By similarity|
|Site||401 – 402||2||Cleavage; by Ty1 protease By similarity|
|Site||582 – 583||2||Cleavage; by Ty1 protease By similarity|
|Site||1217 – 1218||2||Cleavage; by Ty1 protease By similarity|
|||"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII."|
Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. Barrell B.G.
Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
|||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.
|||"Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1 element."|
Wilhelm F.-X., Wilhelm M., Gabriel A.
Cytogenet. Genome Res. 110:269-287(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW, DOMAINS.
|+||Additional computationally mapped references.|
|Z47816 Genomic DNA. Translation: CAA87830.1. Sequence problems.|
BK006946 Genomic DNA. Translation: DAA09854.1.
|RefSeq||NP_013668.1. NM_001182402.1. |
3D structure databases
Protein-protein interaction databases
|BioGrid||35125. 6 interactions.|
|IntAct||Q04711. 2 interactions.|
Protocols and materials databases
Genome annotation databases
|EnsemblFungi||YML045W; YML045W; YML045W. |
|SGD||S000004508. YML045W. |
Gene expression databases
Family and domain databases
|InterPro||IPR001969. Aspartic_peptidase_AS. |
|Pfam||PF00665. rve. 1 hit. |
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
|SUPFAM||SSF53098. SSF53098. 1 hit. |
|PROSITE||PS00141. ASP_PROTEASE. 1 hit. |
PS50994. INTEGRASE. 1 hit.
|Accession||Primary (citable) accession number: Q04711|
Secondary accession number(s): D6VZD0
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Fungal Protein Annotation Program|
|Yeast chromosome XIII|
Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
Index of protein domains and families
Classification of peptidase families and list of entries