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Q7LHG5

- YI31B_YEAST

UniProt

Q7LHG5 - YI31B_YEAST

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Protein

Transposon Ty3-I Gag-Pol polyprotein

Gene

TY3B-I

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 genomic RNA-nucleocapsid complex.By similarity
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).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).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).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei207 – 2082Cleavage; by Ty3 protease
Sitei233 – 2342Cleavage; by Ty3 protease
Sitei309 – 3102Cleavage; by Ty3 protease
Active sitei336 – 3361For protease activity; shared with dimeric partnerBy similarity
Sitei442 – 4432Cleavage; by Ty3 proteaseSequence Analysis
Sitei561 – 5622Cleavage; by Ty3 protease
Metal bindingi712 – 7121Magnesium; catalytic; for reverse transcriptase activityBy similarity
Metal bindingi774 – 7741Magnesium; catalytic; for reverse transcriptase activityBy similarity
Metal bindingi775 – 7751Magnesium; catalytic; for reverse transcriptase activityBy similarity
Sitei1037 – 10382Cleavage; by Ty3 protease
Sitei1063 – 10642Cleavage; by Ty3 protease; partial
Metal bindingi1201 – 12011Magnesium; catalytic; for integrase activityBy similarity
Metal bindingi1262 – 12621Magnesium; catalytic; for integrase activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri265 – 28218CCHC-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. ATP binding Source: UniProtKB-KW
  3. DNA binding Source: UniProtKB-KW
  4. DNA-directed DNA polymerase activity Source: SGD
  5. peptidase activity Source: SGD
  6. ribonuclease activity Source: SGD
  7. RNA binding Source: SGD
  8. RNA-directed DNA polymerase activity Source: SGD
  9. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC
  10. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA-dependent DNA replication Source: GOC
  2. DNA integration Source: UniProtKB-KW
  3. DNA recombination Source: UniProtKB-KW
  4. RNA-dependent DNA replication Source: GOC
  5. RNA phosphodiester bond hydrolysis 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, 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 Ty3-I Gag-Pol polyprotein
Alternative name(s):
Gag3-Pol3
Transposon Ty3-2 TYA-TYB polyprotein
Cleaved into the following 8 chains:
Capsid protein
Short name:
CA
Alternative name(s):
p24
Ty3 protease (EC:3.4.23.-)
Short name:
PR
Alternative name(s):
p16
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):
p55
Integrase p52
Short name:
IN
Integrase p49
Short name:
IN
Gene namesi
Name:TY3B-I
Synonyms:YILWTy3-1 POL
Ordered Locus Names:YIL082W-A
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IX

Organism-specific databases

SGDiS000003537. YIL082W-A.

Subcellular locationi

Cytoplasm. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  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 – 14981498Transposon Ty3-I Gag-Pol polyproteinPRO_0000279367Add
BLAST
Chaini1 – 207207Capsid proteinPRO_0000279368Add
BLAST
Peptidei208 – 23326Spacer peptide p3PRO_0000279369Add
BLAST
Chaini234 – 30976Nucleocapsid protein p11PRO_0000279370Add
BLAST
Chaini310 – 442133Ty3 proteasePRO_0000279371Add
BLAST
Peptidei443 – 561119Spacer peptide JSequence AnalysisPRO_0000279372Add
BLAST
Chaini562 – 1037476Reverse transcriptase/ribonuclease HPRO_0000279373Add
BLAST
Chaini1038 – 1498461Integrase p52PRO_0000279374Add
BLAST
Chaini1064 – 1498435Integrase p49PRO_0000279375Add
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, 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).By similarity

Expressioni

Gene expression databases

GenevestigatoriQ7LHG5.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi34910. 5 interactions.
IntActiQ7LHG5. 3 interactions.
MINTiMINT-541560.

Structurei

3D structure databases

ProteinModelPortaliQ7LHG5.
SMRiQ7LHG5. Positions 576-1037, 1137-1359.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini646 – 823178Reverse transcriptasePROSITE-ProRule annotationAdd
BLAST
Domaini919 – 1037119RNase H Ty3/gyspy-typeAdd
BLAST
Domaini1185 – 1350166Integrase catalyticPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1132 – 117140Integrase-type zinc finger-likeAdd
BLAST

Domaini

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).By similarity

Sequence similaritiesi

Contains 1 CCHC-type zinc finger.PROSITE-ProRule annotation
Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 peptidase A2 domain.Curated
Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri265 – 28218CCHC-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000172599.
InParanoidiQ7LHG5.
KOiK07497.
OrthoDBiEOG7HF1TD.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR001584. 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]
PfamiPF12384. Peptidase_A2B. 1 hit.
PF03732. Retrotrans_gag. 1 hit.
PF00665. rve. 1 hit.
PF00078. RVT_1. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMiSSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50994. INTEGRASE. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 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.

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

        10         20         30         40         50
MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML
60 70 80 90 100
NMSMISWPND ASRIVYCRRH LLNPAAQWAN DFVQEQGILE ITFDTFIQGL
110 120 130 140 150
YQHFYKPPDI NKIFNAITQL SEAKLGIERL NQRFRKIWDR MPPDFMTEKA
160 170 180 190 200
AIMTYTRLLT KETYNIVRMH KPETLKDAME EAYQTTALTE RFFPGFELDA
210 220 230 240 250
DGDTIIGATT HLQEEYDSDY DSEDNLTQNR YVHTVRTRRS YNKPMSNHRN
260 270 280 290 300
RRNNNASREE CIKNRLCFYC KKEGHRLNEC RARKAVLTDL ELESKDQQTL
310 320 330 340 350
FIKTLPIVHY IAIPEMDNTA EKTIKIQNTK VKTLFDSGSP TSFIRRDIVE
360 370 380 390 400
LLKYEIYETP PLRFRGFVAT KSAVTSEAVT IDLKINDLQI TLAAYILDNM
410 420 430 440 450
DYQLLIGNPI LRRYPKILHT VLNTRESPDS LKPKTYRSET VNNVRTYSAG
460 470 480 490 500
NRGNPRNIKL SFAPTILEAT DPKSAGNRGN PRNTKLSLAP TILEATDPKS
510 520 530 540 550
AGNRGDSRTK TLSLATTTPA AIDPLTTLDN PGSTQSTFAQ FPIPEEASIL
560 570 580 590 600
EEDGKYSNVV STIQSVEPNA TDHSNKDTFC TLPVWLQQKY REIIRNDLPP
610 620 630 640 650
RPADINNIPV KHDIEIKPGA RLPRLQPYHV TEKNEQEINK IVQKLLDNKF
660 670 680 690 700
IVPSKSPCSS PVVLVPKKDG TFRLCVDYRT LNKATISDPF PLPRIDNLLS
710 720 730 740 750
RIGNAQIFTT LDLHSGYHQI PMEPKDRYKT AFVTPSGKYE YTVMPFGLVN
760 770 780 790 800
APSTFARYMA DTFRDLRFVN VYLDDILIFS ESPEEHWKHL DTVLERLKNE
810 820 830 840 850
NLIVKKKKCK FASEETEFLG YSIGIQKIAP LQHKCAAIRD FPTPKTVKQA
860 870 880 890 900
QRFLGMINYY RRFIPNCSKI AQPIQLFICD KSQWTEKQDK AIEKLKAALC
910 920 930 940 950
NSPVLVPFNN KANYRLTTDA SKDGIGAVLE EVDNKNKLVG VVGYFSKSLE
960 970 980 990 1000
SAQKNYPAGE LELLGIIKAL HHFRYMLHGK HFTLRTDHIS LLSLQNKNEP
1010 1020 1030 1040 1050
ARRVQRWLDD LATYDFTLEY LAGPKNVVAD AISRAIYTIT PETSRPIDTE
1060 1070 1080 1090 1100
SWKSYYKSDP LCSAVLIHMK ELTQHNVTPE DMSAFRSYQK KLELSETFRK
1110 1120 1130 1140 1150
NYSLEDEMIY YQDRLVVPIK QQNAVMRLYH DHTLFGGHFG VTVTLAKISP
1160 1170 1180 1190 1200
IYYWPKLQHS IIQYIRTCVQ CQLIKSHRPR LHGLLQPLPI AEGRWLDISM
1210 1220 1230 1240 1250
DFVTGLPPTS NNLNMILVVV DRFSKRAHFI ATRKTLDATQ LIDLLFRYIF
1260 1270 1280 1290 1300
SYHGFPRTIT SDRDVRMTAD KYQELTKRLG IKSTMSSANH PQTDGQSERT
1310 1320 1330 1340 1350
IQTLNRLLRA YVSTNIQNWH VYLPQIEFVY NSTPTRTLGK SPFEIDLGYL
1360 1370 1380 1390 1400
PNTPAIKSDD EVNARSFTAV ELAKHLKALT IQTKEQLEHA QIEMETNNNQ
1410 1420 1430 1440 1450
RRKPLLLNIG DHVLVHRDAY FKKGAYMKVQ QIYVGPFRVV KKINDNAYEL
1460 1470 1480 1490
DLNSHKKKHR VINVQFLKSL YTVQTRTQRI NQSAPLRELR EHTKLLHS

Note: Produced by +1 ribosomal frameshifting between codon Ala-285 and Val-286 of the YIL082W ORF.

Length:1,498
Mass (Da):172,369
Last modified:March 6, 2007 - v2
Checksum:i4E51C3EFBDEFD7E4
GO
Isoform Transposon Ty3-I Gag polyprotein (identifier: Q99219-1) [UniParc]FASTAAdd to Basket

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.

Length:290
Mass (Da):34,100
GO

Sequence cautioni

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.

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti502 – 5021G → A in AAA35184. (PubMed:2854194)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiS53577.
RefSeqiNP_012184.1. NM_001181434.3.

Genome annotation databases

GeneIDi854728.
KEGGisce:YIL082W-A.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRi S53577.
RefSeqi NP_012184.1. NM_001181434.3.

3D structure databases

ProteinModelPortali Q7LHG5.
SMRi Q7LHG5. Positions 576-1037, 1137-1359.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34910. 5 interactions.
IntActi Q7LHG5. 3 interactions.
MINTi MINT-541560.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 854728.
KEGGi sce:YIL082W-A.

Organism-specific databases

SGDi S000003537. YIL082W-A.

Phylogenomic databases

HOGENOMi HOG000172599.
InParanoidi Q7LHG5.
KOi K07497.
OrthoDBi EOG7HF1TD.

Miscellaneous databases

NextBioi 977418.

Gene expression databases

Genevestigatori Q7LHG5.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR001584. 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 ]
Pfami PF12384. Peptidase_A2B. 1 hit.
PF03732. Retrotrans_gag. 1 hit.
PF00665. rve. 1 hit.
PF00078. RVT_1. 1 hit.
[Graphical view ]
SMARTi SM00343. ZnF_C2HC. 1 hit.
[Graphical view ]
SUPFAMi SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEi PS50994. INTEGRASE. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

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

Entry informationi

Entry nameiYI31B_YEAST
AccessioniPrimary (citable) accession number: Q7LHG5
Secondary accession number(s): D6VVK4
, Q04717, Q04722, Q05350
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 6, 2007
Last modified: October 29, 2014
This is version 95 of the entry and version 2 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. 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.

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

External Data

Dasty 3