Q12414 · YP11B_YEAST

Function

function

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.
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).

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. Ty1 retrotransposons belong to the copia elements (pseudoviridae).

Catalytic activity

Features

Showing features for site, active site, binding site.

TypeIDPosition(s)Description
Site401-402Cleavage; by Ty1 protease
Active site461For protease activity; shared with dimeric partner
Site582-583Cleavage; by Ty1 protease
Binding site671Mg2+ 1 (UniProtKB | ChEBI); catalytic; for integrase activity
Binding site736Mg2+ 1 (UniProtKB | ChEBI); catalytic; for integrase activity
Site1217-1218Cleavage; by Ty1 protease
Binding site1346Mg2+ 2 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity
Binding site1427Mg2+ 2 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity
Binding site1428Mg2+ 2 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity
Binding site1610Mg2+ 3 (UniProtKB | ChEBI); catalytic; for RNase H activity
Binding site1652Mg2+ 3 (UniProtKB | ChEBI); catalytic; for RNase H activity
Binding site1685Mg2+ 3 (UniProtKB | ChEBI); catalytic; for RNase H activity

GO annotations

AspectTerm
Cellular Componentcytoplasm
Cellular Componentnucleus
Molecular Functionaspartic-type endopeptidase activity
Molecular FunctionATP binding
Molecular FunctionDNA binding
Molecular FunctionDNA-directed DNA polymerase activity
Molecular Functionmetal ion binding
Molecular FunctionRNA binding
Molecular FunctionRNA-directed DNA polymerase activity
Molecular FunctionRNA-DNA hybrid ribonuclease activity
Biological ProcessDNA integration
Biological ProcessDNA recombination
Biological Processproteolysis
Biological Processtransposition
Biological Processviral translational frameshifting

Keywords

Names & Taxonomy

Protein names

Gene names

    • Name
      TY1B-PL
    • Synonyms
      YPLWTy1-1 POL
    • ORF names
      P0729
    • Ordered locus names
      YPL257W-B

Organism names

Accessions

  • Primary accession
    Q12414
  • Secondary accessions
    • D6W3B2

Proteomes

Organism-specific databases

Subcellular Location

Keywords

PTM/Processing

Features

Showing features for chain, modified residue.

TypeIDPosition(s)Description
ChainPRO_00002791701-401Capsid protein
ChainPRO_00002791691-1755Transposon Ty1-PL Gag-Pol polyprotein
ChainPRO_0000279171402-582Ty1 protease
Modified residue416Phosphoserine
ChainPRO_0000279172583-1217Integrase
ChainPRO_00002791731218-1755Reverse transcriptase/ribonuclease H

Post-translational modification

Initially, virus-like particles (VLPs) are composed of the structural unprocessed proteins Gag and Gag-Pol, and also contain 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).

Keywords

Proteomic databases

Interaction

Subunit

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).

Protein-protein interaction databases

Miscellaneous

Structure

Family & Domains

Features

Showing features for compositional bias, region, domain, motif.

TypeIDPosition(s)Description
Compositional bias1-36Polar residues
Region1-93Disordered
Compositional bias47-67Polar residues
Compositional bias71-85Pro residues
Region126-174Disordered
Compositional bias131-164Polar residues
Region299-401RNA-binding
Region352-421Disordered
Compositional bias360-374Basic and acidic residues
Compositional bias375-421Polar residues
Region583-640Integrase-type zinc finger-like
Domain660-835Integrase catalytic
Region956-1087Disordered
Compositional bias969-983Basic and acidic residues
Compositional bias993-1018Polar residues
Compositional bias1040-1056Basic and acidic residues
Compositional bias1057-1080Polar residues
Region1092-1111Disordered
Compositional bias1097-1111Polar residues
Region1130-1187Disordered
Compositional bias1134-1148Pro residues
Compositional bias1153-1178Polar residues
Motif1178-1212Bipartite nuclear localization signal
Domain1338-1476Reverse transcriptase Ty1/copia-type
Domain1610-1752RNase H Ty1/copia-type

Domain

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-x35-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).

Keywords

Phylogenomic databases

Family and domain databases

Sequence & Isoform

Align isoforms (2)
  • Sequence status
    Complete

This entry describes 2 isoforms produced by Ribosomal frameshifting. 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).

Q12414-1

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.

  • Name
    Transposon Ty1-PL Gag-Pol polyprotein
  • Note
    Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YPL257W-A ORF.
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Length
    1,755
  • Mass (Da)
    198,576
  • Last updated
    1996-11-01 v1
  • Checksum
    C1D766C7C6070422
MESQQLSQHSPISHGSACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMIPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLTSPNDFPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDILSVDYTDIMKILSKSIEKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIIDRLNNNGIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTVAELFLDIHAIYEEQQGSRNSKPNYRRNLSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARAHNVSTSNNSPSTDNDSISKSTTEPIQLNNKHDLHLGQELTESTVNHTNHSDDELPGHLLLDSGASRTLIRSAHHIHSASSNPDINVVDAQKRNIPINAIGDLQFHFQDNTKTSIKVLHTPNIAYDLLSLNELAAVDITACFTKNVLERSDGTVLAPIVKYGDFYWVSKKYLLPSNISVPTINNVHTSESTRKYPYPFIHRMLAHANAQTIRYSLKNNTITYFNESDVDWSSAIDYQCPDCLIGKSTKHRHIKGSRLKYQNSYEPFQYLHTDIFGPVHNLPNSAPSYFISFTDETTKFRWVYPLHDRREDSILDVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDCRTQLQCSGLPNHLWFSAIEFSTIVRNSLASPKSKKSARQHAGLAGLDISTLLPFGQPVIVNDHNPNSKIHPRGIPGYALHPSRNSYGYIIYLPSLKKTVDTTNYVILQGKESRLDQFNYDALTFDEDLNRLTASYHSFIASNEIQESNDLNIESDHDFQSDIELHPEQPRNVLSKAVSPTDSTPPSTHTEDSKRVSKTNIRAPREVDPNISESNILPSKKRSSTPQISNIESTGSGGMHKLNVPLLAPMSQSNTHESSHASKSKDFRHSDSYSENETNHTNVPISSTGGTNNKTVPQISDQETEKRIIHRSPSIDASPPENNSSHNIVPIKTPTTVSEQNTEESIIADLPLPDLPPESPTEFPDPFKELPPINSRQTNSSLGGIGDSNAYTTINSKKRSLEDNETEIKVSRDTWNTKNMRSLEPPRSKKRIHLIAAVKAVKSIKPIRTTLRYDEAITYNKDIKEKEKYIEAYHKEVNQLLKMKTWDTDEYYDRKEIDPKRVINSMFIFNKKRDGTHKARFVARGDIQHPDTYDSGMQSNTVHHYALMTSLSLALDNNYYITQLDISSAYLYADIKEELYIRPPPHLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQCGMEEVRGWSCVFKNSQVTICLFVDDMILFSKDLNANKKIITTLKKQYDTKIINLGESDNEIQYDILGLEIKYQRGKYMKLGMENSLTEKIPKLNVPLNPKGRKLSAPGQPGLYIDQDELEIDEDEYKEKVHEMQKLIGLASYVGYKFRFDLLYYINTLAQHILFPSRQVLDMTYELIQFMWDTRDKQLIWHKNKPTEPDNKLVAISDASYGNQPYYKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELNKKPIIKGLLTDSRSTISIIKSTNEEKFRNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLPIKTFKLLTNKWIH

P0CX73-1

The sequence of this isoform can be found in the external entry linked below. Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

View isoform
  • Name
    Transposon Ty1-PL Gag polyprotein
  • See also
    sequence in UniParc or sequence clusters in UniRef

Features

Showing features for compositional bias.

TypeIDPosition(s)Description
Compositional bias1-36Polar residues
Compositional bias47-67Polar residues
Compositional bias71-85Pro residues
Compositional bias131-164Polar residues
Compositional bias360-374Basic and acidic residues
Compositional bias375-421Polar residues
Compositional bias969-983Basic and acidic residues
Compositional bias993-1018Polar residues
Compositional bias1040-1056Basic and acidic residues
Compositional bias1057-1080Polar residues
Compositional bias1097-1111Polar residues
Compositional bias1134-1148Pro residues
Compositional bias1153-1178Polar residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
Z73613
EMBL· GenBank· DDBJ
CAA97984.1
EMBL· GenBank· DDBJ
Genomic DNA
Z73614
EMBL· GenBank· DDBJ
CAA97988.1
EMBL· GenBank· DDBJ
Genomic DNA
BK006949
EMBL· GenBank· DDBJ
DAA11178.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

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