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O13535

- YH11B_YEAST

UniProt

O13535 - YH11B_YEAST

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Protein
Transposon Ty1-H Gag-Pol polyprotein
Gene
TY1B-H, YHRCTy1-1 POL, YHR214C-B
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

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 activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei439 – 4402Cleavage; by Ty1 protease By similarity
Active sitei499 – 4991For protease activity; shared with dimeric partner By similarity
Sitei620 – 6212Cleavage; by Ty1 protease By similarity
Metal bindingi709 – 7091Magnesium; catalytic; for integrase activity By similarity
Metal bindingi774 – 7741Magnesium; catalytic; for integrase activity By similarity
Sitei1255 – 12562Cleavage; by Ty1 protease By similarity
Metal bindingi1384 – 13841Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1465 – 14651Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1466 – 14661Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1648 – 16481Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1690 – 16901Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1723 – 17231Magnesium; catalytic; for RNase H activity By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. DNA-directed DNA polymerase activity Source: SGD
  4. RNA binding Source: SGD
  5. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC
  6. RNA-directed DNA polymerase activity Source: SGD
  7. aspartic-type endopeptidase activity Source: UniProtKB-KW
  8. metal ion binding Source: UniProtKB-KW
  9. peptidase activity Source: SGD
  10. 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. transposition, RNA-mediated Source: SGD
  7. viral release from host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Transposition, Virion maturation, Virus exit from host cell

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Transposon Ty1-H Gag-Pol polyprotein
Alternative name(s):
Gag-Pol-p199
TY1A-TY1B
Transposon Ty1 TYA-TYB polyprotein
p190
Cleaved into the following 4 chains:
Capsid protein
Short name:
CA
Alternative name(s):
Gag-p45
p54
Ty1 protease (EC:3.4.23.-)
Short name:
PR
Alternative name(s):
Pol-p20
p23
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-H
Synonyms:YHRCTy1-1 POL
Ordered Locus Names:YHR214C-B
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VIII

Organism-specific databases

CYGDiYHR214c-b.
SGDiS000003534. YHR214C-B.

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 – 17931793Transposon Ty1-H Gag-Pol polyprotein
PRO_0000279074Add
BLAST
Chaini1 – 439439Capsid protein By similarity
PRO_0000279075Add
BLAST
Chaini440 – 620181Ty1 protease By similarity
PRO_0000279076Add
BLAST
Chaini621 – 1255635Integrase By similarity
PRO_0000279077Add
BLAST
Chaini1256 – 1793538Reverse transcriptase/ribonuclease H By similarity
PRO_0000279078Add
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

GenevestigatoriO13535.

Interactioni

Subunit structurei

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

BioGridi36648. 7 interactions.
IntActiO13535. 3 interactions.
MINTiMINT-7544181.
STRINGi4932.YHR214C-B.

Structurei

3D structure databases

ProteinModelPortaliO13535.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini698 – 873176Integrase catalytic
Add
BLAST
Domaini1376 – 1514139Reverse transcriptase Ty1/copia-type
Add
BLAST
Domaini1648 – 1790143RNase H Ty1/copia-type
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni337 – 439103RNA-binding By similarity
Add
BLAST
Regioni621 – 67858Integrase-type zinc finger-like
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1216 – 125035Bipartite nuclear localization signal By similarity
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi72 – 14675Pro-rich
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

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00730000111405.
HOGENOMiHOG000280731.
OrthoDBiEOG7TJ3S3.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamiPF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

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-H Gag-Pol polyprotein (identifier: O13535-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MESQQLSNYP HISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA     50
NSQQTTTPAS SAVPENLHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG 100
WSFYGHPSMI PYTPYQMSPM YFPPGPQSQF PQYPSSVGTP LSTPSPESGN 150
TFTDSSSADS DMTSTKKYVR PPPMLTSPND FPNWVKTYIK FLQNSNLGGI 200
IPTVNGKPVP PMLTSPNDFP NWVKTYIKFL QNSNLGGIIP TVNGKPVRQI 250
TDDELTFLYN TFQIFAPSQF LPTWVKDILS VDYTDIMKIL SKSIEKMQSD 300
TQEANDIVTL ANLQYNGSTP ADAFETKVTN IIDRLNNNGI HINNKVACQL 350
IMRGLSGEYK FLRYTRHRHL NMTVAELFLD IHAIYEEQQG SRNSKPNYRR 400
NPSDEKNDSR SYTNTTKPKV IARNPQKTNN SKSKTARAHN VSTSNNSPST 450
DNDSISKSTT EPIQLNNKHD LHLGQKLTES TVNHTNHSDD ELPGHLLLDS 500
GASRTLIRSA HHIHSASSNP DINVVDAQKR NIPINAIGDL QFHFQDNTKT 550
SIKVLHTPNI AYDLLSLNEL AAVDITACFT KNVLERSDGT VLAPIVKYGD 600
FYWVSKKYLL PSNISVPTIN NVHTSESTRK YPYPFIHRML AHANAQTIRY 650
SLKNNTITYF NESDVDWSSA IDYQCPDCLI GKSTKHRHIK GSRLKYQNSY 700
EPFQYLHTDI FGPVHNLPKS APSYFISFTD ETTKFRWVYP LHDRREDSIL 750
DVFTTILAFI KNQFQASVLV IQMDRGSEYT NRTLHKFLEK NGITPCYTTT 800
ADSRAHGVAE RLNRTLLDDC RTQLQCSGLP NHLWFSAIEF STIVRNSLAS 850
PKSKKSARQH AGLAGLDIST LLPFGQPVIV NDHNPNSKIH PRGIPGYALH 900
PSRNSYGYII YLPSLKKTVD TTNYVILQGK ESRLDQFNYD ALTFDEDLNR 950
LTASYHSFIA SNEIQQSNDL NIESDHDFQS DIELHPEQLR NVLSKAVSPT 1000
DSTPPSTHTE DSKRVSKTNI RAPREVDPNI SESNILPSKK RSSTPQISDI 1050
ESTGSGGMHR LDVPLLAPMS QSNTHESSHA SKSKDFRHSD SYSDNETNHT 1100
NVPISSTGGT NNKTVPQTSE QETEKRIIHR SPSIDTSSSE SNSLHHVVPI 1150
KTSDTCPKEN TEESIIADLP LPDLPPEPPT ELSDSFKELP PINSHQTNSS 1200
LGGIGDSNAY TTINSKKRSL EDNETEIKVS RDTWNTKNMR SLEPPRSKKR 1250
IHLIAAVKAV KSIKPIRTTL RYDEAITYNK DIKEKEKYIQ AYHKEVNQLL 1300
MMKTWDTDRY YDRKEIDPKR VINSMFIFNR KRDGTHKARF VARGDIQHPD 1350
TYDPGMQSNT VHHYALMTSL SLALDNNYYI TQLDISSAYL YADIKEELYI 1400
RPPPHLGMND KLIRLKKSLY GLKQSGANWY ETIKSYLIKQ CGMEEVRGWS 1450
CVFKNSQVTI CLFVDDMILF SKDLNANKKI ITTLKKQYDT KIINLGESDN 1500
EIQYDILGLE IKYQRGKYMK LGMENSLTEK IPKLNVPLNP KGRKLSAPGQ 1550
PGLYIDQDEL EIDEDEYKEK VHEMQKLIGL ASYVGYKFRF DLLYYINTLA 1600
QHILFPSRQV LDMTYELIQF MWDTRDKQLI WHKNKPTEPD NKLVAISDAS 1650
YGNQPYYKSQ IGNIYLLNGK VIGGKSTKAS LTCTSTTEAE IHAISESVPL 1700
LNNLSHLVQE LNKKPITKGL LTDSKSTISI IISNNEEKFR NRFFGTKAMR 1750
LRDEVSGNHL HVCYIETKKN IADVMTKPLP IKTFKLLTNK WIH 1793

Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YHR214C-C ORF.

Length:1,793
Mass (Da):202,817
Last modified:January 1, 1998 - v1
Checksum:i1DA6A07E10E0A2CB
GO
Isoform Transposon Ty1-H Gag polyprotein (identifier: P0C2I4-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry P0C2I4.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:478
Mass (Da):53,325
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00029 Genomic DNA. Translation: AAB69744.1.
BK006934 Genomic DNA. Translation: DAA06910.1.
PIRiS40969.
S52601.
RefSeqiNP_012086.1. NM_001181431.1. [O13535-1]

Genome annotation databases

EnsemblFungiiYHR214C-B; YHR214C-B; YHR214C-B. [O13535-1]
GeneIDi856623.
KEGGisce:YHR214C-B.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00029 Genomic DNA. Translation: AAB69744.1 .
BK006934 Genomic DNA. Translation: DAA06910.1 .
PIRi S40969.
S52601.
RefSeqi NP_012086.1. NM_001181431.1. [O13535-1 ]

3D structure databases

ProteinModelPortali O13535.
ModBasei Search...

Protein-protein interaction databases

BioGridi 36648. 7 interactions.
IntActi O13535. 3 interactions.
MINTi MINT-7544181.
STRINGi 4932.YHR214C-B.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YHR214C-B ; YHR214C-B ; YHR214C-B . [O13535-1 ]
GeneIDi 856623.
KEGGi sce:YHR214C-B.

Organism-specific databases

CYGDi YHR214c-b.
SGDi S000003534. YHR214C-B.

Phylogenomic databases

GeneTreei ENSGT00730000111405.
HOGENOMi HOG000280731.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 982559.

Gene expression databases

Genevestigatori O13535.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR001969. Aspartic_peptidase_AS.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view ]
Pfami PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view ]
SUPFAMi SSF53098. SSF53098. 1 hit.
PROSITEi PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. 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.

Entry informationi

Entry nameiYH11B_YEAST
AccessioniPrimary (citable) accession number: O13535
Secondary accession number(s): D3DLG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: January 1, 1998
Last modified: May 14, 2014
This is version 102 of the entry and version 1 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).

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

Documents

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

External Data

Dasty 3

Similar proteinsi