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P0C2I5 (YL12B_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 58. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Transposon Ty1-LR2 Gag-Pol polyprotein
Alternative name(s):
Gag-Pol-p199
TY1A-TY1B
Transposon Ty1 TYA-TYB polyprotein
p190

Cleaved into the following 4 chains:

  1. Capsid protein
    Short name=CA
    Alternative name(s):
    Gag-p45
    p54
  2. Ty1 protease
    Short name=PR
    EC=3.4.23.-
    Alternative name(s):
    Pol-p20
    p23
  3. Integrase
    Short name=IN
    Alternative name(s):
    Pol-p71
    p84
    p90
  4. Reverse transcriptase/ribonuclease H
    Short name=RT
    EC=2.7.7.49
    EC=2.7.7.7
    EC=3.1.26.4
    Alternative name(s):
    Pol-p63
    p60
Gene names
Name:TY1B-LR2
Synonyms:YLRCTy1-2 POL
Ordered Locus Names:YLR157C-B
ORF Names:L9632.7
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length1755 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

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 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.

Catalytic activity

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Endonucleolytic cleavage to 5'-phosphomonoester.

Subunit structure

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.

Subcellular location

Cytoplasm. Nucleus By similarity.

Domain

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

Post-translational modification

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.

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).

Sequence similarities

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.

Ontologies

Keywords
   Biological processDNA integration
DNA recombination
Transposition
Virion maturation
Virus exit from host cell
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityRibosomal frameshifting
   DomainZinc-finger
   LigandATP-binding
DNA-binding
Magnesium
Metal-binding
Nucleotide-binding
RNA-binding
Zinc
   Molecular functionAspartyl protease
DNA-directed DNA polymerase
Endonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Protease
RNA-directed DNA polymerase
Transferase
   PTMPhosphoprotein
   Technical termComplete proteome
Multifunctional enzyme
Reference proteome
Transposable element
Gene Ontology (GO)
   Biological_processDNA integration

Inferred from electronic annotation. Source: UniProtKB-KW

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-dependent DNA replication

Inferred from sequence or structural similarity Ref.3. Source: GOC

RNA phosphodiester bond hydrolysis

Inferred from sequence or structural similarity Ref.3. Source: GOC

RNA-dependent DNA replication

Inferred from sequence or structural similarity Ref.3. Source: GOC

proteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

transposition, RNA-mediated

Inferred from sequence or structural similarity Ref.3. Source: SGD

viral release from host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay PubMed 9448009. Source: SGD

retrotransposon nucleocapsid

Inferred from sequence or structural similarity Ref.3. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-directed DNA polymerase activity

Inferred from sequence or structural similarity Ref.3. Source: SGD

RNA binding

Inferred from sequence or structural similarity Ref.3. Source: SGD

RNA-DNA hybrid ribonuclease activity

Inferred from electronic annotation. Source: UniProtKB-EC

RNA-directed DNA polymerase activity

Inferred from sequence or structural similarity Ref.3. Source: SGD

aspartic-type endopeptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

peptidase activity

Inferred from sequence or structural similarity Ref.3. Source: SGD

ribonuclease activity

Inferred from sequence or structural similarity Ref.3. Source: SGD

Complete GO annotation...

Alternative products

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-LR2 Gag-Pol polyprotein (identifier: P0C2I5-1)

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 YLR157C-A ORF.
Isoform Transposon Ty1-LR2 Gag polyprotein (identifier: P0CX72-1)

The sequence of this isoform can be found in the external entry P0CX72.
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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17551755Transposon Ty1-LR2 Gag-Pol polyprotein
PRO_0000279099
Chain1 – 401401Capsid protein By similarity
PRO_0000279100
Chain402 – 582181Ty1 protease By similarity
PRO_0000279101
Chain583 – 1217635Integrase By similarity
PRO_0000279102
Chain1218 – 1755538Reverse transcriptase/ribonuclease H By similarity
PRO_0000279103

Regions

Domain660 – 835176Integrase catalytic
Domain1338 – 1476139Reverse transcriptase Ty1/copia-type
Domain1610 – 1752143RNase H Ty1/copia-type
Region299 – 401103RNA-binding By similarity
Region583 – 64058Integrase-type zinc finger-like
Motif1178 – 121235Bipartite nuclear localization signal By similarity
Compositional bias64 – 14683Pro-rich

Sites

Active site4611For protease activity; shared with dimeric partner By similarity
Metal binding6711Magnesium; catalytic; for integrase activity By similarity
Metal binding7361Magnesium; catalytic; for integrase activity By similarity
Metal binding13461Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding14271Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding14281Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding16101Magnesium; catalytic; for RNase H activity By similarity
Metal binding16521Magnesium; catalytic; for RNase H activity By similarity
Metal binding16851Magnesium; catalytic; for RNase H activity By similarity
Site401 – 4022Cleavage; by Ty1 protease By similarity
Site582 – 5832Cleavage; by Ty1 protease By similarity
Site1217 – 12182Cleavage; by Ty1 protease By similarity

Amino acid modifications

Modified residue4161Phosphoserine By similarity

Sequences

Sequence LengthMass (Da)Tools
Isoform Transposon Ty1-LR2 Gag-Pol polyprotein [UniParc].

Last modified March 6, 2007. Version 1.
Checksum: 2916CADCA298D8A7

FASTA1,755198,545
        10         20         30         40         50         60 
MESQQLSQHS PISHGSACAS VTSKEVHTNQ DPLDVSASKT EECEKASTKA NSQQTTTPAS 

        70         80         90        100        110        120 
SAVPENPHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG WSFYGHPSMI PYTPYQMSPM 

       130        140        150        160        170        180 
YFPPGPQSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND 

       190        200        210        220        230        240 
FPNWVKTYIK FLQNSNLGGI IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI 

       250        260        270        280        290        300 
LSVDYTDIMK ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN 

       310        320        330        340        350        360 
GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ QGSRNSKPNY 

       370        380        390        400        410        420 
RRNLSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA HNVSTSNNSP STDNDSISKS 

       430        440        450        460        470        480 
TTEPIQLNNK HDLHLGQELT ESTVNHTNHS DDELPGHLLL DSGASRTLIR SAHHIHSASS 

       490        500        510        520        530        540 
NPDINVVDAQ KRNIPINAIG DLQFHFQDNT KTSIKVLHTP NIAYDLLSLN ELAAVDITAC 

       550        560        570        580        590        600 
FTKNVLERSD GTVLAPIVKY GDFYWVSKKY LLPSNISVPT INNVHTSEST RKYPYPFIHR 

       610        620        630        640        650        660 
MLAHANAPTI RYSLKNNTIT YFNESDVDWS SAIDYQCPDC LIGKSTKHRH IKGSRLKYQN 

       670        680        690        700        710        720 
SYEPFQYLHT DIFGPVHNLP NSAPSYFISF TDETTKFRWV YPLHDRREDS ILDVFTTILA 

       730        740        750        760        770        780 
FIKNQFQASV LVIQMDRGSE YTNRTLHKFL EKNGITPCYT TTADSRAHGV AERLNRTLLD 

       790        800        810        820        830        840 
DCRTQLQCSG LPNHLWFSAI EFSTIVRNSL ASPKSKKSAR QHAGLAGLDI STLLPFGQPV 

       850        860        870        880        890        900 
IVNDHNPNSK IHPRGIPGYA LHPSRNSYGY IIYLPSLKKT VDTTNYVILQ GKESRLDQFN 

       910        920        930        940        950        960 
YDALTFDEDL NRLTASYHSF IASNEIQESN DLNIESDHDF QSDIELHPEQ PRNVLSKAVS 

       970        980        990       1000       1010       1020 
PTDSTPPSTH TEDSKRVSKT NIRAPREVDP NISESNILPS KKRSSTPQIS NIESTGSGGM 

      1030       1040       1050       1060       1070       1080 
HKLNVPLLAP MSQSNTHESS HASKSKDFRH SDSYSENETN HTNVPISSTG GTNNKTVPQI 

      1090       1100       1110       1120       1130       1140 
SDQETEKRII HRSPSIDASP PENNSSHNIV PIKTPTTVSE QNTEESIIAD LPLPDLPPES 

      1150       1160       1170       1180       1190       1200 
PTEFPDPFKE LPPINSRQTN SSLGGIGDSN AYTTINSKKR SLEDNETEIK VSRDTWNTKN 

      1210       1220       1230       1240       1250       1260 
MRSLEPPRSK KRIHLIAAVK AVKSIKPIRT TLRYDEAITY NKDIKEKEKY IEAYHKEVNQ 

      1270       1280       1290       1300       1310       1320 
LLKMKTWDTD EYYDRKEIDP KRVINSMFIF NKKRDGTHKA RFVARGDIQH PDTYDSGMQS 

      1330       1340       1350       1360       1370       1380 
NTVHHYALMT SLSLALDNNY YITQLDISSA YLYADIKEEL YIRPPPHLGM NDKLIRLKKS 

      1390       1400       1410       1420       1430       1440 
LYGLKQSGAN WYETIKSYLI KQCGMEEVRG WSCVFKNSQV TICLFVDDMI LFSKDLNANK 

      1450       1460       1470       1480       1490       1500 
KIITTLKKQY DTKIINLGES DNEIQYDILG LEIKYQRGKY MKLGMENSLT EKIPKLNVPL 

      1510       1520       1530       1540       1550       1560 
NPKGRKLSAP GQPGLYIDQD ELEIDEDEYK EKVHEMQKLI GLASYVGYKF RFDLLYYINT 

      1570       1580       1590       1600       1610       1620 
LAQHILFPSR QVLDMTYELI QFMWDTRDKQ LIWHKNKPTE PDNKLVAISD ASYGNQPYYK 

      1630       1640       1650       1660       1670       1680 
SQIGNIYLLN GKVIGGKSTK ASLTCTSTTE AEIHAISESV PLLNNLSYLI QELNKKPIIK 

      1690       1700       1710       1720       1730       1740 
GLLTDSRSTI SIIKSTNEEK FRNRFFGTKA MRLRDEVSGN NLYVYYIETK KNIADVMTKP 

      1750 
LPIKTFKLLT NKWIH 

« Hide

Isoform Transposon Ty1-LR2 Gag polyprotein [UniParc].

See P0CX72.

References

« Hide 'large scale' references
[1]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. expand/collapse author list , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[3]"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.
[4]"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.
[5]"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U51921 Genomic DNA. No translation available.
BK006945 Genomic DNA. Translation: DAA09474.1.
PIRS69960.
RefSeqNP_058169.1. NM_001184406.1.

3D structure databases

ProteinModelPortalP0C2I5.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31429. 7 interactions.
IntActP0C2I5. 10 interactions.
STRING4932.YLR157C-B.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLR157C-B; YLR157C-B; YLR157C-B. [P0C2I5-1]
GeneID850853.
KEGGsce:YLR157C-B.

Organism-specific databases

SGDS000007374. YLR157C-B.

Phylogenomic databases

GeneTreeENSGT00730000111405.
HOGENOMHOG000280731.
OrthoDBEOG7TJ3S3.

Gene expression databases

GenevestigatorP0C2I5.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
InterProIPR001969. Aspartic_peptidase_AS.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamPF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view]
SUPFAMSSF53098. SSF53098. 1 hit.
PROSITEPS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio967158.

Entry information

Entry nameYL12B_YEAST
AccessionPrimary (citable) accession number: P0C2I5
Secondary accession number(s): D6VYF8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 6, 2007
Last modified: April 16, 2014
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XII

Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries