Q7LHG5 (YI31B_YEAST) Reviewed, UniProtKB/Swiss-Prot
Last modified July 9, 2014. Version 93. History...
Names and origin
|Protein names||Recommended name:|
Transposon Ty3-I Gag-Pol polyprotein
Transposon Ty3-2 TYA-TYB polyprotein
Cleaved into the following 8 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||1498 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 genomic RNA-nucleocapsid complex By similarity. Ref.4
Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers By similarity. Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 RNA and initiation of reverse transcription By similarity. Ref.4
The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP By similarity. Ref.4
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. Ref.4
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. Ref.4
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.
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. Ty3 retrotransposons belong to the gypsy-like elements (metaviridae).
In contrast to Ty3-1 (Ty3-G), Ty3-2 (Ty3-I) is a transpositionally inactive element. The Ty3-2 ORF is truncated by the deletion of a single nucleotide, which causes a frameshift mutation when compared with Ty3-1.
Contains 1 CCHC-type zinc finger.
Contains 1 integrase catalytic domain.
Contains 1 peptidase A2 domain.
Contains 1 reverse transcriptase domain.
Contains 1 RNase H Ty3/gyspy-type domain.
The sequence AAA35184.1 differs from that shown. Reason: Erroneous gene model prediction.
The sequence CAA86713.1 differs from that shown. Reason: Erroneous gene model prediction.
The sequence DAA08470.1 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.
|Isoform Transposon Ty3-I Gag-Pol polyprotein (identifier: Q7LHG5-1) |
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 Ala-285 and Val-286 of the YIL082W ORF.|
|Isoform Transposon Ty3-I Gag polyprotein (identifier: Q99219-1) |
The sequence of this isoform can be found in the external entry Q99219.
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 – 1498||1498||Transposon Ty3-I Gag-Pol polyprotein||PRO_0000279367|
|Chain||1 – 207||207||Capsid protein||PRO_0000279368|
|Peptide||208 – 233||26||Spacer peptide p3||PRO_0000279369|
|Chain||234 – 309||76||Nucleocapsid protein p11||PRO_0000279370|
|Chain||310 – 442||133||Ty3 protease||PRO_0000279371|
|Peptide||443 – 561||119||Spacer peptide J Potential||PRO_0000279372|
|Chain||562 – 1037||476||Reverse transcriptase/ribonuclease H||PRO_0000279373|
|Chain||1038 – 1498||461||Integrase p52||PRO_0000279374|
|Chain||1064 – 1498||435||Integrase p49||PRO_0000279375|
|Domain||646 – 823||178||Reverse transcriptase|
|Domain||919 – 1037||119||RNase H Ty3/gyspy-type|
|Domain||1185 – 1350||166||Integrase catalytic|
|Zinc finger||265 – 282||18||CCHC-type|
|Region||1132 – 1171||40||Integrase-type zinc finger-like|
|Active site||336||1||For protease activity; shared with dimeric partner By similarity|
|Metal binding||712||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||774||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||775||1||Magnesium; catalytic; for reverse transcriptase activity By similarity|
|Metal binding||1201||1||Magnesium; catalytic; for integrase activity By similarity|
|Metal binding||1262||1||Magnesium; catalytic; for integrase activity By similarity|
|Site||207 – 208||2||Cleavage; by Ty3 protease|
|Site||233 – 234||2||Cleavage; by Ty3 protease|
|Site||309 – 310||2||Cleavage; by Ty3 protease|
|Site||442 – 443||2||Cleavage; by Ty3 protease Potential|
|Site||561 – 562||2||Cleavage; by Ty3 protease|
|Site||1037 – 1038||2||Cleavage; by Ty3 protease|
|Site||1063 – 1064||2||Cleavage; by Ty3 protease; partial|
|Sequence conflict||502||1||G → A in AAA35184. Ref.1|
|||"Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses."|
Hansen L.J., Chalker D.L., Sandmeyer S.B.
Mol. Cell. Biol. 8:5245-5256(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
|||"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX."|
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. Barrell B.G.
Nature 387:84-87(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
|||"The reference genome sequence of Saccharomyces cerevisiae: Then and now."|
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
|||"Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein."|
Hansen L.J., Sandmeyer S.B.
J. Virol. 64:2599-2607(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
|||"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.|
|M23367 Genomic DNA. Translation: AAA35184.1. Sequence problems.|
Z46728 Genomic DNA. Translation: CAA86713.1. Sequence problems.
Z37997 Genomic DNA. Translation: CAA86090.1.
BK006942 Genomic DNA. Translation: DAA08470.1. Sequence problems.
|RefSeq||NP_012184.1. NM_001181434.3. |
3D structure databases
|SMR||Q7LHG5. Positions 576-1037, 1137-1359. |
Protein-protein interaction databases
|BioGrid||34910. 5 interactions.|
|IntAct||Q7LHG5. 3 interactions.|
Protocols and materials databases
Genome annotation databases
|SGD||S000003537. YIL082W-A. |
Gene expression databases
Family and domain databases
|Gene3D||3.30.420.10. 1 hit. |
|InterPro||IPR001584. Integrase_cat-core. |
|Pfam||PF12384. Peptidase_A2B. 1 hit. |
PF03732. Retrotrans_gag. 1 hit.
PF00665. rve. 1 hit.
PF00078. RVT_1. 1 hit.
|SMART||SM00343. ZnF_C2HC. 1 hit. |
|SUPFAM||SSF50630. SSF50630. 1 hit. |
SSF53098. SSF53098. 1 hit.
SSF57756. SSF57756. 1 hit.
|PROSITE||PS50994. INTEGRASE. 1 hit. |
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.
|Accession||Primary (citable) accession number: Q7LHG5|
Secondary accession number(s): D6VVK4 Q05350
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Fungal Protein Annotation Program|
|Yeast chromosome IX|
Yeast (Saccharomyces cerevisiae) chromosome IX: 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