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Q99337

- YN12B_YEAST

UniProt

Q99337 - YN12B_YEAST

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Protein

Transposon Ty1-NL2 Gag-Pol polyprotein

Gene

TY1B-NL2

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).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).
Endonucleolytic cleavage to 5'-phosphomonoester.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei401 – 4022Cleavage; by Ty1 proteaseBy similarity
Active sitei461 – 4611For protease activity; shared with dimeric partnerPROSITE-ProRule annotation
Sitei582 – 5832Cleavage; by Ty1 proteaseBy similarity
Metal bindingi671 – 6711Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Metal bindingi736 – 7361Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Sitei1211 – 12122Cleavage; by Ty1 proteaseBy similarity
Metal bindingi1340 – 13401Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1421 – 14211Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1422 – 14221Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1604 – 16041Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1646 – 16461Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1679 – 16791Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation

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. metal ion binding Source: UniProtKB-KW
  6. peptidase activity Source: SGD
  7. ribonuclease activity Source: SGD
  8. RNA binding Source: SGD
  9. RNA-directed DNA polymerase activity Source: SGD
  10. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

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, 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-NL2 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-NL2
Synonyms:YNLWTy1-2 POL
Ordered Locus Names:YNL054W-B
ORF Names:N2453
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIV

Organism-specific databases

CYGDiYNL054w-b.
SGDiS000007385. YNL054W-B.

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 – 17491749Transposon Ty1-NL2 Gag-Pol polyproteinPRO_0000279145Add
BLAST
Chaini1 – 401401Capsid proteinBy similarityPRO_0000279146Add
BLAST
Chaini402 – 582181Ty1 proteaseBy similarityPRO_0000279147Add
BLAST
Chaini583 – 1211629IntegraseBy similarityPRO_0000279148Add
BLAST
Chaini1212 – 1749538Reverse transcriptase/ribonuclease HBy similarityPRO_0000279149Add
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).By similarity

Proteomic databases

PaxDbiQ99337.

Expressioni

Gene expression databases

GenevestigatoriQ99337.

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).By similarity

Protein-protein interaction databases

DIPiDIP-9004N.
IntActiQ99337. 4 interactions.
MINTiMINT-529254.

Structurei

3D structure databases

ProteinModelPortaliQ99337.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini660 – 835176Integrase catalyticPROSITE-ProRule annotationAdd
BLAST
Domaini1332 – 1470139Reverse transcriptase Ty1/copia-typeAdd
BLAST
Domaini1604 – 1746143RNase H Ty1/copia-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni299 – 401103RNA-bindingBy similarityAdd
BLAST
Regioni583 – 64058Integrase-type zinc finger-likeAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1172 – 120635Bipartite nuclear localization signalBy similarityAdd
BLAST

Domaini

The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities.By similarity
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 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 peptidase A11 domain.Curated

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG283194.
InParanoidiQ99337.
OrthoDBiEOG7PK96X.

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).By similarity

Isoform Transposon Ty1-NL2 Gag-Pol polyprotein (identifier: Q99337-1) [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

        10         20         30         40         50
MESQQLSQHS PISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA
60 70 80 90 100
NSQQTTTPAS SAVPENPHHA SPQTAQSHSP QNGPYPQQCM MTQNQANPSD
110 120 130 140 150
WSFYGRPSMI PYTPYQMSPM YFPPGPHSQF PQYPSSVGTP LSTPSPESGN
160 170 180 190 200
TFTDSSSADS DMTSTKKYVR PPPMLTSPND FLNWVKTYIK FLQNSNLGGI
210 220 230 240 250
IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI LSVDYTDIMK
260 270 280 290 300
ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN
310 320 330 340 350
GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ
360 370 380 390 400
QGSRNSKPNY RRNPSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA
410 420 430 440 450
HNVSTSNNSP STDNDSISKS TTEPIQLNNK HDLHLGQKLT ESTVNHTNHS
460 470 480 490 500
DDELPGHLLL DSGASRTLIR SAHHIHSASS NPDINVVDAQ KRNIPINAIG
510 520 530 540 550
DLQFHFQDNT KTSIKVLHTP NIAYDLLSLN ELAAVDITAC FTKNVLERSD
560 570 580 590 600
GTVLAPIVKY GDFYWVSKKY LLPSNISVPT INNVHTSEST RKYPYPFIHR
610 620 630 640 650
MLAHANAQTI RYSLKNNTIT YFNESDVDWS SAIDYQCPDC LIGKSTKHRH
660 670 680 690 700
IKGSRLKYQN SYEPFQYLHT DIFGPVHNLP KSAPSYFISF TDETTKFRWV
710 720 730 740 750
YPLHDRREDS ILDVFTTILA FIKNQFQASV LVIQMDRGSE YTNRTLHKFL
760 770 780 790 800
EKNGITPCYT TTADSRAHGV AERLNRTLLD DCRTQLQCSG LPNHLWFSAI
810 820 830 840 850
EFSTIVRNSL ASPKSKKSAR QHAGLAGLDI STLLPFGQPV IVNDHNPNSK
860 870 880 890 900
IHPRGIPGYA LHPSRNSYGY IIYLPSLKKT VDTTNYVILQ GKESRLDQFN
910 920 930 940 950
YDALTFDEDL NRLTASYQSF IASNEIQQSD DLNFQSDIEL HPEQPRNVLS
960 970 980 990 1000
KAVSPTDSTP PSTHTEDSKR VSKTNIRAPR EVDPNISKSD ILPSKKRSST
1010 1020 1030 1040 1050
PQISDIESTG SGGMHRLDVP LLAPMSQSNT HESSHTSKSK DFRHSDSYSD
1060 1070 1080 1090 1100
NETNHTNVPI SSTGGTNNKT VPQTSEQETE KRIIHRSPSI DTSSSESNSL
1110 1120 1130 1140 1150
HHVVPIKTSD TCPKENTEES IIADLPLPDL PPEPPTKLSD SFKELPPINS
1160 1170 1180 1190 1200
RQTNSSLGGI GDSNAYTTIN SKKRSLEDNE TEIKVSRDTW NTKNMRSLEP
1210 1220 1230 1240 1250
PRSKKRIHLI AAVKAVKSIK PIRTTLRYDE AITYNKDIKE KEKYIEAYHK
1260 1270 1280 1290 1300
EVNQLLKMKT WDTDKYYDRK EIDPKRVINS MFIFNRKRDG THKARFVARG
1310 1320 1330 1340 1350
DIQHPDTYDS GMQSNTVHHY ALMTSLSLAL DNNYYITQLD ISSAYLYADI
1360 1370 1380 1390 1400
KEELYIRPPP HLGMNDKLIR LKKSLYGLKQ SGANWYETIK SYLIEQCDME
1410 1420 1430 1440 1450
EVRGWSCVFK NSQVTICLFV DDMILFSKDL NANKKIITTL KKQYDTKIIN
1460 1470 1480 1490 1500
LGESDNEIQY DILGLEIKYQ RSKYMKLGME KSLTEKLPKL NVHLNPKGKK
1510 1520 1530 1540 1550
LSAPGQPGLY IDQDELEIDE DEYKEKVHEM QKLIGLASYV GYKFRFDLLY
1560 1570 1580 1590 1600
YINTLAQHIL FPSRQVLDMT YELIQFMWDT RDKQLIWHKN KPTKPDNKLV
1610 1620 1630 1640 1650
AISDASYGNQ PYYKSQIGNI FLLNGKVIGG KSTKASLTCT STTEAEIHAV
1660 1670 1680 1690 1700
SEAIPLLNNL SHLVQELNKK PIIKGLLTDS RSTISIIKST NEEKFRNRFF
1710 1720 1730 1740
GTKAMRLRDE VSGNNLYVYY IETKKNIADV MTKPLPIKTF KLLTNKWIH

Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YNL054W-A ORF.

Length:1,749
Mass (Da):198,198
Last modified:November 1, 1996 - v1
Checksum:iB837BC682F22DFE5
GO
Isoform Transposon Ty1-NL2 Gag polyprotein (identifier: Q12470-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q12470.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:440
Mass (Da):49,232
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71331 Genomic DNA. Translation: CAA95928.1.
Z71330 Genomic DNA. Translation: CAA95924.1.
BK006947 Genomic DNA. Translation: DAA64521.1.
PIRiS69972.
RefSeqiNP_001268465.1. NM_001281536.1. [Q99337-1]

Genome annotation databases

GeneIDi855672.
KEGGisce:YNL054W-B.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71331 Genomic DNA. Translation: CAA95928.1 .
Z71330 Genomic DNA. Translation: CAA95924.1 .
BK006947 Genomic DNA. Translation: DAA64521.1 .
PIRi S69972.
RefSeqi NP_001268465.1. NM_001281536.1. [Q99337-1 ]

3D structure databases

ProteinModelPortali Q99337.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9004N.
IntActi Q99337. 4 interactions.
MINTi MINT-529254.

Proteomic databases

PaxDbi Q99337.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 855672.
KEGGi sce:YNL054W-B.

Organism-specific databases

CYGDi YNL054w-b.
SGDi S000007385. YNL054W-B.

Phylogenomic databases

eggNOGi NOG283194.
InParanoidi Q99337.
OrthoDBi EOG7PK96X.

Gene expression databases

Genevestigatori Q99337.

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. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    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 nameiYN12B_YEAST
AccessioniPrimary (citable) accession number: Q99337
Secondary accession number(s): S6G3B3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: November 1, 1996
Last modified: October 29, 2014
This is version 95 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

External Data

Dasty 3