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O13527 (YA11B_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Truncated transposon Ty1-A Gag-Pol polyprotein
Alternative name(s):
TY1B
Transposon Ty1 TYB polyprotein

Cleaved into the following 2 chains:

  1. Integrase
    Short name=IN
    Alternative name(s):
    Pol-p71
    p84
    p90
  2. Reverse transcriptase/ribonuclease H
    Short name=RT
    Short name=RT-RH
    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-A
Synonyms:YARCTy1-1 POL
Ordered Locus Names:YAR009C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length1196 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

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.

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.6

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.6

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 reverse transcriptase Ty1/copia-type domain.

Contains 1 RNase H Ty1/copia-type domain.

Caution

Transposon Ty1-A (YARCTy1-1) contains a frameshift at position 610, which disrupts the ORF coding for protein TY1B. This is the truncated, C-terminal part of TY1B translated from an in-frame start codon, and it is probably not functional.

Ontologies

Keywords
   Biological processDNA integration
DNA recombination
Transposition
   Cellular componentCytoplasm
Nucleus
   LigandDNA-binding
Magnesium
Metal-binding
RNA-binding
   Molecular functionDNA-directed DNA polymerase
Endonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
RNA-directed DNA polymerase
Transferase
   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.4. Source: GOC

RNA phosphodiester bond hydrolysis

Inferred from sequence or structural similarity Ref.4. Source: GOC

RNA-dependent DNA replication

Inferred from sequence or structural similarity Ref.4. Source: GOC

proteolysis

Inferred from sequence or structural similarity Ref.4. Source: GOC

transposition, RNA-mediated

Inferred from sequence or structural similarity Ref.4. Source: SGD

   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.4. Source: SGD

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-directed DNA polymerase activity

Inferred from sequence or structural similarity Ref.4. Source: SGD

RNA binding

Inferred from sequence or structural similarity Ref.4. 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.4. Source: SGD

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

peptidase activity

Inferred from sequence or structural similarity Ref.4. Source: SGD

ribonuclease activity

Inferred from sequence or structural similarity Ref.4. Source: SGD

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 11961196Truncated transposon Ty1-A Gag-Pol polyprotein
PRO_0000278977
Chain1 – 658658Integrase By similarity
PRO_0000278980
Chain659 – 1196538Reverse transcriptase/ribonuclease H By similarity
PRO_0000278981

Regions

Domain101 – 276176Integrase catalytic
Domain779 – 917139Reverse transcriptase Ty1/copia-type
Domain1051 – 1193143RNase H Ty1/copia-type
Motif619 – 65335Bipartite nuclear localization signal By similarity

Sites

Metal binding1121Magnesium; catalytic; for integrase activity By similarity
Metal binding1771Magnesium; catalytic; for integrase activity By similarity
Metal binding7871Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding8681Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding8691Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding10511Magnesium; catalytic; for RNase H activity By similarity
Metal binding10931Magnesium; catalytic; for RNase H activity By similarity
Metal binding11261Magnesium; catalytic; for RNase H activity By similarity
Site658 – 6592Cleavage; by Ty1 protease By similarity

Sequences

Sequence LengthMass (Da)Tools
O13527 [UniParc].

Last modified November 2, 2010. Version 3.
Checksum: 0A3E8CFC5B12C6A2

FASTA1,196136,732
        10         20         30         40         50         60 
METFTGYLKS TCFHQISPYP PSIMSIQVKV HANILILSFI ECLRMPMHRQ IRYSLKNNTI 

        70         80         90        100        110        120 
TYFNESDVDW SSAIDYQCPD CLIGKSTKHR HIKGSRLKYQ NSYEPFQYLH TDIFGPVHNL 

       130        140        150        160        170        180 
PKSAPSYFIS FTDETTKLRW VYPLHDRRED SILDVFTTIL AFIKNQFQAS VLVIQMDRGS 

       190        200        210        220        230        240 
EYTNRTLHKF LEKNGITPCY TTTADSRAHG VAERLNRTLL DDCRTQLQCS GLPNHLWFSA 

       250        260        270        280        290        300 
IEFSTIVRNS LASPKSKKSA RQHAGLAGLD ISTLLPFGQP VIVNDHNPNS KIHPRGIPGY 

       310        320        330        340        350        360 
ALHPSRNSYG YIIYLPSLKK TVDTTNYVIL QGKESRLDQF NYDALTFDED LNRLTASYHS 

       370        380        390        400        410        420 
FIASNEIQES NDLNIESDHD FQSDIELHPE QPRNVLSKAV SPTDSTPPST HTEDSKRVSK 

       430        440        450        460        470        480 
TNIRAPREVD PNISESNILP SKKRSSTPQI SNIESTGSGG MHKLNVPLLA PMSQSNTHES 

       490        500        510        520        530        540 
SHASKSKDFR HSDSYSENET NHTNVPISST GGTNNKTVPQ ISDQETEKRI IHRSPSIDAS 

       550        560        570        580        590        600 
PPENNSSHNI VPIKTPTTVS EQNTEESIIA DLPLPDLPPE SPTEFPDPFK ELPPINSHQT 

       610        620        630        640        650        660 
NSSLGGIGDS NAYTTINSKK RSLEDNETEI KVSRDTWNTK NMRSLEPPRS KKRIHLIAAV 

       670        680        690        700        710        720 
KAVKSIKPIR TTLRYDEAIT YNKDIKEKEK YIEAYHKEVN QLLKMNTWDT DKYYDRKEID 

       730        740        750        760        770        780 
PKRVINSMFI FNKKRDGTHK ARFVARGDIQ HPDTYDTGMQ SNTVHHYALM TSLSLALDNN 

       790        800        810        820        830        840 
YYITQLDISS AYLYADIKEE LYIRPPPHLG MNDKLIRLKK SLYGLKQSGA NWYETIKSYL 

       850        860        870        880        890        900 
IKQCGMEEVR GWSCVFKNSQ VTICLFVDDM ILFSKDLNAN KKIITTLKKQ YDTKIINLGE 

       910        920        930        940        950        960 
SDNEIQYDIL GLEIKYQRGK YMKLGMEKSL TEKLPKLNVP LNPKGKKLRA PGQPGLYIDQ 

       970        980        990       1000       1010       1020 
DELEIDEDEY KEKVHEMQKL IGLASYVGYK FRFDLLYYIN TLAQHILFPS RQVLDMTYEL 

      1030       1040       1050       1060       1070       1080 
IQFMWDTRDK QLIWHKNKPT EPDNKLVAIS DASYGNQPYY KSQIGNIYLL NGKVIGGKST 

      1090       1100       1110       1120       1130       1140 
KASLTCTSTT EAEIHAISES VPLLNNLSYL IQELNKKPII KGLLTDSRST ISIIKSTNEE 

      1150       1160       1170       1180       1190 
KFRNRFFGTK AMRLRDEVSG NNLYVYYIET KKNIADVMTK PLPIKTFKLL TNKWIH 

« Hide

References

« Hide 'large scale' references
[1]"Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region."
Clark M.W., Keng T., Storms R.K., Zhong W.-W., Fortin N., Zeng B., Delaney S., Ouellette B.F.F., Barton A.B., Kaback D.B., Bussey H.
Yeast 10:535-541(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[2]"The nucleotide sequence of chromosome I from Saccharomyces cerevisiae."
Bussey H., Kaback D.B., Zhong W.-W., Vo D.H., Clark M.W., Fortin N., Hall J., Ouellette B.F.F., Keng T., Barton A.B., Su Y., Davies C.J., Storms R.K.
Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"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.
[4]"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, IDENTIFICATION OF FRAMESHIFT.
[5]"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.
[6]"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
L22015 Genomic DNA. Translation: AAC04967.1.
BK006935 Genomic DNA. Translation: DAA06991.1.
PIRS40908.
RefSeqNP_009406.1. NM_001178213.1.

3D structure databases

ProteinModelPortalO13527.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31795. 8 interactions.
DIPDIP-2632N.
IntActO13527. 2 interactions.
MINTMINT-601384.
STRING4932.YPR137C-B.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYAR009C; YAR009C; YAR009C.
GeneID851268.
KEGGsce:YAR009C.

Organism-specific databases

CYGDYAR009c.
SGDS000000067. YAR009C.

Phylogenomic databases

GeneTreeENSGT00730000111405.
OMANINLQEE.
OrthoDBEOG7TJ3S3.

Gene expression databases

GenevestigatorO13527.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
InterProIPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamPF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
[Graphical view]
SUPFAMSSF53098. SSF53098. 1 hit.
PROSITEPS50994. INTEGRASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio968240.

Entry information

Entry nameYA11B_YEAST
AccessionPrimary (citable) accession number: O13527
Secondary accession number(s): D6VPM1
Entry history
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: November 2, 2010
Last modified: May 14, 2014
This is version 103 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome I

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

Yeast

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

SIMILARITY comments

Index of protein domains and families