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Q7LHG5 (YI31B_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 93. 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 Ty3-I Gag-Pol polyprotein
Alternative name(s):
Gag3-Pol3
Transposon Ty3-2 TYA-TYB polyprotein

Cleaved into the following 8 chains:

  1. Capsid protein
    Short name=CA
    Alternative name(s):
    p24
  2. Spacer peptide p3
  3. Nucleocapsid protein p11
    Short name=NC
  4. Ty3 protease
    Short name=PR
    EC=3.4.23.-
    Alternative name(s):
    p16
  5. Spacer peptide J
  6. 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):
    p55
  7. Integrase p52
    Short name=IN
  8. Integrase p49
    Short name=IN
Gene names
Name:TY3B-I
Synonyms:YILWTy3-1 POL
Ordered Locus Names:YIL082W-A
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length1498 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 genomic RNA-nucleocapsid complex By similarity. Ref.4

Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers By similarity. Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 RNA and initiation of reverse transcription By similarity. Ref.4

The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP By similarity. Ref.4

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. Ref.4

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. Ref.4

Catalytic activity

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

Endonucleolytic cleavage to 5'-phosphomonoester.

Subunit structure

The protease is a homodimer, whose active site consists of two apposed aspartic acid residues By similarity.

Subcellular location

Cytoplasm. Nucleus By similarity.

Domain

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.

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, and this cleavage is a prerequisite for subsequent processing 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. Ty3 retrotransposons belong to the gypsy-like elements (metaviridae).

In contrast to Ty3-1 (Ty3-G), Ty3-2 (Ty3-I) is a transpositionally inactive element. The Ty3-2 ORF is truncated by the deletion of a single nucleotide, which causes a frameshift mutation when compared with Ty3-1.

Sequence similarities

Contains 1 CCHC-type zinc finger.

Contains 1 integrase catalytic domain.

Contains 1 peptidase A2 domain.

Contains 1 reverse transcriptase domain.

Contains 1 RNase H Ty3/gyspy-type domain.

Sequence caution

The sequence AAA35184.1 differs from that shown. Reason: Erroneous gene model prediction.

The sequence CAA86713.1 differs from that shown. Reason: Erroneous gene model prediction.

The sequence DAA08470.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
   Biological processDNA integration
DNA recombination
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
   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.5. Source: GOC

RNA phosphodiester bond hydrolysis

Inferred from sequence or structural similarity Ref.5. Source: GOC

transposition, RNA-mediated

Inferred from sequence or structural similarity Ref.5. 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.5. 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.5. Source: SGD

RNA binding

Inferred from sequence or structural similarity Ref.5. 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.5. Source: SGD

aspartic-type endopeptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

peptidase activity

Inferred from sequence or structural similarity Ref.5. Source: SGD

ribonuclease activity

Inferred from sequence or structural similarity Ref.5. Source: SGD

zinc ion binding

Inferred from electronic annotation. Source: InterPro

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.
Isoform Transposon Ty3-I Gag-Pol polyprotein (identifier: Q7LHG5-1)

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 Ala-285 and Val-286 of the YIL082W ORF.
Isoform Transposon Ty3-I Gag polyprotein (identifier: Q99219-1)

The sequence of this isoform can be found in the external entry Q99219.
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 – 14981498Transposon Ty3-I Gag-Pol polyprotein
PRO_0000279367
Chain1 – 207207Capsid protein
PRO_0000279368
Peptide208 – 23326Spacer peptide p3
PRO_0000279369
Chain234 – 30976Nucleocapsid protein p11
PRO_0000279370
Chain310 – 442133Ty3 protease
PRO_0000279371
Peptide443 – 561119Spacer peptide J Potential
PRO_0000279372
Chain562 – 1037476Reverse transcriptase/ribonuclease H
PRO_0000279373
Chain1038 – 1498461Integrase p52
PRO_0000279374
Chain1064 – 1498435Integrase p49
PRO_0000279375

Regions

Domain646 – 823178Reverse transcriptase
Domain919 – 1037119RNase H Ty3/gyspy-type
Domain1185 – 1350166Integrase catalytic
Zinc finger265 – 28218CCHC-type
Region1132 – 117140Integrase-type zinc finger-like

Sites

Active site3361For protease activity; shared with dimeric partner By similarity
Metal binding7121Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding7741Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding7751Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding12011Magnesium; catalytic; for integrase activity By similarity
Metal binding12621Magnesium; catalytic; for integrase activity By similarity
Site207 – 2082Cleavage; by Ty3 protease
Site233 – 2342Cleavage; by Ty3 protease
Site309 – 3102Cleavage; by Ty3 protease
Site442 – 4432Cleavage; by Ty3 protease Potential
Site561 – 5622Cleavage; by Ty3 protease
Site1037 – 10382Cleavage; by Ty3 protease
Site1063 – 10642Cleavage; by Ty3 protease; partial

Experimental info

Sequence conflict5021G → A in AAA35184. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform Transposon Ty3-I Gag-Pol polyprotein [UniParc].

Last modified March 6, 2007. Version 2.
Checksum: 4E51C3EFBDEFD7E4

FASTA1,498172,369
        10         20         30         40         50         60 
MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND 

        70         80         90        100        110        120 
ASRIVYCRRH LLNPAAQWAN DFVQEQGILE ITFDTFIQGL YQHFYKPPDI NKIFNAITQL 

       130        140        150        160        170        180 
SEAKLGIERL NQRFRKIWDR MPPDFMTEKA AIMTYTRLLT KETYNIVRMH KPETLKDAME 

       190        200        210        220        230        240 
EAYQTTALTE RFFPGFELDA DGDTIIGATT HLQEEYDSDY DSEDNLTQNR YVHTVRTRRS 

       250        260        270        280        290        300 
YNKPMSNHRN RRNNNASREE CIKNRLCFYC KKEGHRLNEC RARKAVLTDL ELESKDQQTL 

       310        320        330        340        350        360 
FIKTLPIVHY IAIPEMDNTA EKTIKIQNTK VKTLFDSGSP TSFIRRDIVE LLKYEIYETP 

       370        380        390        400        410        420 
PLRFRGFVAT KSAVTSEAVT IDLKINDLQI TLAAYILDNM DYQLLIGNPI LRRYPKILHT 

       430        440        450        460        470        480 
VLNTRESPDS LKPKTYRSET VNNVRTYSAG NRGNPRNIKL SFAPTILEAT DPKSAGNRGN 

       490        500        510        520        530        540 
PRNTKLSLAP TILEATDPKS AGNRGDSRTK TLSLATTTPA AIDPLTTLDN PGSTQSTFAQ 

       550        560        570        580        590        600 
FPIPEEASIL EEDGKYSNVV STIQSVEPNA TDHSNKDTFC TLPVWLQQKY REIIRNDLPP 

       610        620        630        640        650        660 
RPADINNIPV KHDIEIKPGA RLPRLQPYHV TEKNEQEINK IVQKLLDNKF IVPSKSPCSS 

       670        680        690        700        710        720 
PVVLVPKKDG TFRLCVDYRT LNKATISDPF PLPRIDNLLS RIGNAQIFTT LDLHSGYHQI 

       730        740        750        760        770        780 
PMEPKDRYKT AFVTPSGKYE YTVMPFGLVN APSTFARYMA DTFRDLRFVN VYLDDILIFS 

       790        800        810        820        830        840 
ESPEEHWKHL DTVLERLKNE NLIVKKKKCK FASEETEFLG YSIGIQKIAP LQHKCAAIRD 

       850        860        870        880        890        900 
FPTPKTVKQA QRFLGMINYY RRFIPNCSKI AQPIQLFICD KSQWTEKQDK AIEKLKAALC 

       910        920        930        940        950        960 
NSPVLVPFNN KANYRLTTDA SKDGIGAVLE EVDNKNKLVG VVGYFSKSLE SAQKNYPAGE 

       970        980        990       1000       1010       1020 
LELLGIIKAL HHFRYMLHGK HFTLRTDHIS LLSLQNKNEP ARRVQRWLDD LATYDFTLEY 

      1030       1040       1050       1060       1070       1080 
LAGPKNVVAD AISRAIYTIT PETSRPIDTE SWKSYYKSDP LCSAVLIHMK ELTQHNVTPE 

      1090       1100       1110       1120       1130       1140 
DMSAFRSYQK KLELSETFRK NYSLEDEMIY YQDRLVVPIK QQNAVMRLYH DHTLFGGHFG 

      1150       1160       1170       1180       1190       1200 
VTVTLAKISP IYYWPKLQHS IIQYIRTCVQ CQLIKSHRPR LHGLLQPLPI AEGRWLDISM 

      1210       1220       1230       1240       1250       1260 
DFVTGLPPTS NNLNMILVVV DRFSKRAHFI ATRKTLDATQ LIDLLFRYIF SYHGFPRTIT 

      1270       1280       1290       1300       1310       1320 
SDRDVRMTAD KYQELTKRLG IKSTMSSANH PQTDGQSERT IQTLNRLLRA YVSTNIQNWH 

      1330       1340       1350       1360       1370       1380 
VYLPQIEFVY NSTPTRTLGK SPFEIDLGYL PNTPAIKSDD EVNARSFTAV ELAKHLKALT 

      1390       1400       1410       1420       1430       1440 
IQTKEQLEHA QIEMETNNNQ RRKPLLLNIG DHVLVHRDAY FKKGAYMKVQ QIYVGPFRVV 

      1450       1460       1470       1480       1490 
KKINDNAYEL DLNSHKKKHR VINVQFLKSL YTVQTRTQRI NQSAPLRELR EHTKLLHS 

« Hide

Isoform Transposon Ty3-I Gag polyprotein [UniParc].

See Q99219.

References

« Hide 'large scale' references
[1]"Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses."
Hansen L.J., Chalker D.L., Sandmeyer S.B.
Mol. Cell. Biol. 8:5245-5256(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX."
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. expand/collapse author list , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:84-87(1997) [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]"Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein."
Hansen L.J., Sandmeyer S.B.
J. Virol. 64:2599-2607(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[5]"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.
[6]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M23367 Genomic DNA. Translation: AAA35184.1. Sequence problems.
Z46728 Genomic DNA. Translation: CAA86713.1. Sequence problems.
Z37997 Genomic DNA. Translation: CAA86090.1.
BK006942 Genomic DNA. Translation: DAA08470.1. Sequence problems.
PIRS53577.
RefSeqNP_012184.1. NM_001181434.3.

3D structure databases

ProteinModelPortalQ7LHG5.
SMRQ7LHG5. Positions 576-1037, 1137-1359.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34910. 5 interactions.
IntActQ7LHG5. 3 interactions.
MINTMINT-541560.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID854728.
KEGGsce:YIL082W-A.

Organism-specific databases

SGDS000003537. YIL082W-A.

Phylogenomic databases

HOGENOMHOG000172599.
KOK07497.
OrthoDBEOG7HF1TD.

Gene expression databases

GenevestigatorQ7LHG5.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
InterProIPR001584. Integrase_cat-core.
IPR024650. Peptidase_A2B.
IPR021109. Peptidase_aspartic_dom.
IPR005162. Retrotrans_gag_dom.
IPR012337. RNaseH-like_dom.
IPR000477. RT_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PfamPF12384. Peptidase_A2B. 1 hit.
PF03732. Retrotrans_gag. 1 hit.
PF00665. rve. 1 hit.
PF00078. RVT_1. 1 hit.
[Graphical view]
SMARTSM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMSSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEPS50994. INTEGRASE. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio977418.

Entry information

Entry nameYI31B_YEAST
AccessionPrimary (citable) accession number: Q7LHG5
Secondary accession number(s): D6VVK4 expand/collapse secondary AC list , Q04717, Q04722, Q05350
Entry history
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 6, 2007
Last modified: July 9, 2014
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IX

Yeast (Saccharomyces cerevisiae) chromosome IX: 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