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O13527

- YA11B_YEAST

UniProt

O13527 - YA11B_YEAST

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Protein
Truncated transposon Ty1-A Gag-Pol polyprotein
Gene
TY1B-A, YARCTy1-1 POL, YAR009C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

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 activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Endonucleolytic cleavage to 5'-phosphomonoester.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi112 – 1121Magnesium; catalytic; for integrase activity By similarity
Metal bindingi177 – 1771Magnesium; catalytic; for integrase activity By similarity
Sitei658 – 6592Cleavage; by Ty1 protease By similarity
Metal bindingi787 – 7871Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi868 – 8681Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi869 – 8691Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1051 – 10511Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1093 – 10931Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1126 – 11261Magnesium; catalytic; for RNase H activity By similarity

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA-directed DNA polymerase activity Source: SGD
  3. RNA binding Source: SGD
  4. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC
  5. RNA-directed DNA polymerase activity Source: SGD
  6. metal ion binding Source: UniProtKB-KW
  7. peptidase activity Source: SGD
  8. ribonuclease activity Source: SGD
Complete GO annotation...

GO - Biological processi

  1. DNA integration Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. DNA-dependent DNA replication Source: GOC
  4. RNA phosphodiester bond hydrolysis Source: GOC
  5. RNA-dependent DNA replication Source: GOC
  6. proteolysis Source: GOC
  7. transposition, RNA-mediated Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Transposition

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Truncated transposon Ty1-A Gag-Pol polyprotein
Alternative name(s):
TY1B
Transposon Ty1 TYB polyprotein
Cleaved into the following 2 chains:
Integrase
Short name:
IN
Alternative name(s):
Pol-p71
p84
p90
Reverse transcriptase/ribonuclease H (EC:2.7.7.49, EC:2.7.7.7, EC:3.1.26.4)
Short name:
RT
Short name:
RT-RH
Alternative name(s):
Pol-p63
p60
Gene namesi
Name:TY1B-A
Synonyms:YARCTy1-1 POL
Ordered Locus Names:YAR009C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome I

Organism-specific databases

CYGDiYAR009c.
SGDiS000000067. YAR009C.

Subcellular locationi

Cytoplasm. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. nucleus Source: SGD
  3. retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11961196Truncated transposon Ty1-A Gag-Pol polyprotein
PRO_0000278977Add
BLAST
Chaini1 – 658658Integrase By similarity
PRO_0000278980Add
BLAST
Chaini659 – 1196538Reverse transcriptase/ribonuclease H By similarity
PRO_0000278981Add
BLAST

Post-translational modificationi

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.

Expressioni

Gene expression databases

GenevestigatoriO13527.

Interactioni

Protein-protein interaction databases

BioGridi31795. 8 interactions.
DIPiDIP-2632N.
IntActiO13527. 2 interactions.
MINTiMINT-601384.
STRINGi4932.YPR137C-B.

Structurei

3D structure databases

ProteinModelPortaliO13527.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 276176Integrase catalytic
Add
BLAST
Domaini779 – 917139Reverse transcriptase Ty1/copia-type
Add
BLAST
Domaini1051 – 1193143RNase H Ty1/copia-type
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi619 – 65335Bipartite nuclear localization signal By similarity
Add
BLAST

Domaini

The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities By similarity.1 Publication
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,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.1 Publication

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00730000111405.
OMAiNINLQEE.
OrthoDBiEOG7TJ3S3.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamiPF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50994. INTEGRASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O13527-1 [UniParc]FASTAAdd to Basket

« Hide

METFTGYLKS TCFHQISPYP PSIMSIQVKV HANILILSFI ECLRMPMHRQ     50
IRYSLKNNTI TYFNESDVDW SSAIDYQCPD CLIGKSTKHR HIKGSRLKYQ 100
NSYEPFQYLH TDIFGPVHNL PKSAPSYFIS FTDETTKLRW VYPLHDRRED 150
SILDVFTTIL AFIKNQFQAS VLVIQMDRGS EYTNRTLHKF LEKNGITPCY 200
TTTADSRAHG VAERLNRTLL DDCRTQLQCS GLPNHLWFSA IEFSTIVRNS 250
LASPKSKKSA RQHAGLAGLD ISTLLPFGQP VIVNDHNPNS KIHPRGIPGY 300
ALHPSRNSYG YIIYLPSLKK TVDTTNYVIL QGKESRLDQF NYDALTFDED 350
LNRLTASYHS FIASNEIQES NDLNIESDHD FQSDIELHPE QPRNVLSKAV 400
SPTDSTPPST HTEDSKRVSK TNIRAPREVD PNISESNILP SKKRSSTPQI 450
SNIESTGSGG MHKLNVPLLA PMSQSNTHES SHASKSKDFR HSDSYSENET 500
NHTNVPISST GGTNNKTVPQ ISDQETEKRI IHRSPSIDAS PPENNSSHNI 550
VPIKTPTTVS EQNTEESIIA DLPLPDLPPE SPTEFPDPFK ELPPINSHQT 600
NSSLGGIGDS NAYTTINSKK RSLEDNETEI KVSRDTWNTK NMRSLEPPRS 650
KKRIHLIAAV KAVKSIKPIR TTLRYDEAIT YNKDIKEKEK YIEAYHKEVN 700
QLLKMNTWDT DKYYDRKEID PKRVINSMFI FNKKRDGTHK ARFVARGDIQ 750
HPDTYDTGMQ SNTVHHYALM TSLSLALDNN YYITQLDISS AYLYADIKEE 800
LYIRPPPHLG MNDKLIRLKK SLYGLKQSGA NWYETIKSYL IKQCGMEEVR 850
GWSCVFKNSQ VTICLFVDDM ILFSKDLNAN KKIITTLKKQ YDTKIINLGE 900
SDNEIQYDIL GLEIKYQRGK YMKLGMEKSL TEKLPKLNVP LNPKGKKLRA 950
PGQPGLYIDQ DELEIDEDEY KEKVHEMQKL IGLASYVGYK FRFDLLYYIN 1000
TLAQHILFPS RQVLDMTYEL IQFMWDTRDK QLIWHKNKPT EPDNKLVAIS 1050
DASYGNQPYY KSQIGNIYLL NGKVIGGKST KASLTCTSTT EAEIHAISES 1100
VPLLNNLSYL IQELNKKPII KGLLTDSRST ISIIKSTNEE KFRNRFFGTK 1150
AMRLRDEVSG NNLYVYYIET KKNIADVMTK PLPIKTFKLL TNKWIH 1196
Length:1,196
Mass (Da):136,732
Last modified:November 2, 2010 - v3
Checksum:i0A3E8CFC5B12C6A2
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L22015 Genomic DNA. Translation: AAC04967.1.
BK006935 Genomic DNA. Translation: DAA06991.1.
PIRiS40908.
RefSeqiNP_009406.1. NM_001178213.1.

Genome annotation databases

EnsemblFungiiYAR009C; YAR009C; YAR009C.
GeneIDi851268.
KEGGisce:YAR009C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L22015 Genomic DNA. Translation: AAC04967.1 .
BK006935 Genomic DNA. Translation: DAA06991.1 .
PIRi S40908.
RefSeqi NP_009406.1. NM_001178213.1.

3D structure databases

ProteinModelPortali O13527.
ModBasei Search...

Protein-protein interaction databases

BioGridi 31795. 8 interactions.
DIPi DIP-2632N.
IntActi O13527. 2 interactions.
MINTi MINT-601384.
STRINGi 4932.YPR137C-B.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YAR009C ; YAR009C ; YAR009C .
GeneIDi 851268.
KEGGi sce:YAR009C.

Organism-specific databases

CYGDi YAR009c.
SGDi S000000067. YAR009C.

Phylogenomic databases

GeneTreei ENSGT00730000111405.
OMAi NINLQEE.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 968240.

Gene expression databases

Genevestigatori O13527.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view ]
Pfami PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53098. SSF53098. 1 hit.
PROSITEi PS50994. INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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.

Entry informationi

Entry nameiYA11B_YEAST
AccessioniPrimary (citable) accession number: O13527
Secondary accession number(s): D6VPM1
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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).

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.

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome I
    Yeast (Saccharomyces cerevisiae) chromosome I: entries and gene names

External Data

Dasty 3

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