Q07163 (TY1AB_YEASX) Reviewed, UniProtKB/Swiss-Prot
Last modified October 16, 2013. Version 72. History...
Names and origin
|Protein names||Recommended name:|
Transposon TyH3 Gag-Pol polyprotein
Transposon Ty1-H3 TYA-TYB polyprotein
Cleaved into the following 4 chains:
|Organism||Saccharomyces cerevisiae (Baker's yeast)|
|Taxonomic identifier||4932 [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||Evidence at protein 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. 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. Ref.7 Ref.8 Ref.9
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. Ref.7 Ref.8 Ref.9
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. Ref.7 Ref.8 Ref.9
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.
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.
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.
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 AAA66938.1 differs from that shown. Reason: Erroneous gene model prediction.
The sequence CAA25874.1 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.
|Isoform Transposon TyH3 Gag-Pol polyprotein (identifier: Q07163-1) |
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.|
|Isoform Transposon TyH3 Gag polyprotein (identifier: P08405-1) |
The sequence of this isoform can be found in the external entry P08405.
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 TyH3 Gag-Pol polyprotein||PRO_0000278970|
|Chain||1 – 401||401||Capsid protein||PRO_0000278971|
|Chain||402 – 582||181||Ty1 protease||PRO_0000278972|
|Chain||583 – 1217||635||Integrase||PRO_0000278973|
|Chain||1218 – 1755||538||Reverse transcriptase/ribonuclease H||PRO_0000278974|
|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|
|Region||583 – 640||58||Integrase-type zinc finger-like|
|Motif||1178 – 1212||35||Bipartite nuclear localization signal|
|Compositional bias||64 – 146||83||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|
|Site||582 – 583||2||Cleavage; by Ty1 protease|
|Site||1217 – 1218||2||Cleavage; by Ty1 protease|
Amino acid modifications
|Modified residue||416||1||Phosphoserine By similarity|
|Natural variant||12||1||N → I in Ty1-15. Ref.2|
|Natural variant||74 – 79||6||PASVPP → TAQSHS in Ty1-15. |
|Natural variant||142||1||S → R in Ty1-15. Ref.2|
|Mutagenesis||602||1||L → I in Ty173; reduces transposition frequency 60-fold. Ref.1|
|Mutagenesis||1178||1||K → G: Partially prevents nuclear localization of integrase and reduces transposition efficiency by 30%. Prevents nuclear localization of integrase and reduces transposition efficiency by 99.6%; when associated with Gly-1179. Prevents nuclear localization of integrase; when associated with Gly-1179 and Thr-1180. Ref.7|
|Mutagenesis||1179||1||K → G: Prevents nuclear localization of integrase and reduces transposition efficiency by 99.6%; when associated with Gly-1178. Prevents nuclear localization of integrase; when associated with Gly-1178 and Thr-1180. Ref.7|
|Mutagenesis||1180||1||R → T: Prevents nuclear localization of integrase; when associated with Gly-1178 and Gly-1179. Ref.7|
|Mutagenesis||1183 – 1188||6||EDNETE → QNNQTQ: Prevents nuclear localization of integrase. Ref.7|
|Mutagenesis||1210||1||K → G: Reduces transposition efficiency by 77%. Reduces transposition efficiency by 98.4%; when associated with Gly-1211. Reduces transposition efficiency by 99.8%; when associated with Gly-1211 and Thr-1212. Ref.7|
|Mutagenesis||1211||1||K → G: Reduces transposition efficiency by 98.4%; when associated with Gly-1210. Reduces transposition efficiency by 99.8%; when associated with Gly-1210 and Thr-1212. Ref.7|
|Mutagenesis||1212||1||R → T: Reduces transposition efficiency by 99.8%; when associated with Gly-1210 and Gly-1211. Ref.7|
|||"The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1."|
Boeke J.D., Eichinger D., Castrillon D., Fink G.R.
Mol. Cell. Biol. 8:1432-1442(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF LEU-602.
|||"A retrovirus-like strategy for expression of a fusion protein encoded by yeast transposon Ty1."|
Mellor J., Fulton S.M., Dobson M.J., Wilson W., Kingsman S.M., Kingsman A.J.
Nature 313:243-246(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-480, VARIANTS TY1-15 ILE-12; 74-THR--SER-79 AND ARG-142.
|||"Frameshift signal transplantation and the unambiguous analysis of mutations in the yeast retrotransposon Ty1 Gag-Pol overlap region."|
Lawler J.F. Jr., Merkulov G.V., Boeke J.D.
J. Virol. 75:6769-6775(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 402-408, CLEAVAGE SITE HIS-401-402-ASN, MASS SPECTROMETRY.
|||"Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site."|
Belcourt M.F., Farabaugh P.J.
Cell 62:339-352(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: RIBOSOMAL FRAMESHIFT SITE.
|||"Proteolytic processing of pol-TYB proteins from the yeast retrotransposon Ty1."|
Garfinkel D.J., Hedge A.M., Youngren S.D., Copeland T.D.
J. Virol. 65:4573-4581(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING.
|||"Expression and partial purification of enzymatically active recombinant Ty1 integrase in Saccharomyces cerevisiae."|
Moore S.P., Garfinkel D.J.
Proc. Natl. Acad. Sci. U.S.A. 91:1843-1847(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: CLEAVAGE SITES ASN-582-583-ASN AND ALA-1217-1218-ALA.
|||"A Ty1 integrase nuclear localization signal required for retrotransposition."|
Moore S.P., Rinckel L.A., Garfinkel D.J.
Mol. Cell. Biol. 18:1105-1114(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-1178; LYS-1179; ARG-1180; 1183-GLU--GLU-1188; LYS-1210; LYS-1211 AND ARG-1212.
|||"The Gag-like protein of the yeast Ty1 retrotransposon contains a nucleic acid chaperone domain analogous to retroviral nucleocapsid proteins."|
Cristofari G., Ficheux D., Darlix J.-L.
J. Biol. Chem. 275:19210-19217(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, RNA-BINDING.
|||"Polypurine tract formation by Ty1 RNase H."|
Wilhelm M., Uzun O., Mules E.H., Gabriel A., Wilhelm F.-X.
J. Biol. Chem. 276:47695-47701(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
|||"Ty1 proteolytic cleavage sites are required for transposition: all sites are not created equal."|
Merkulov G.V., Lawler J.F. Jr., Eby Y., Boeke J.D.
J. Virol. 75:638-644(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING.
|M18706 Genomic DNA. Translation: AAA66938.1. Sequence problems.|
X01736 Genomic DNA. Translation: CAA25874.1. Sequence problems.
3D structure databases
Protocols and materials databases
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: Q07163|
Secondary accession number(s): Q07169
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Fungal Protein Annotation Program|