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Q12113

- YO21B_YEAST

UniProt

Q12113 - YO21B_YEAST

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Protein
Transposon Ty2-OR1 Gag-Pol polyprotein
Gene
TY2B-OR1, YORCTy2-1 POL, YOR192C-B, O4785
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 Ty2 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
Sitei397 – 3982Cleavage; by Ty2 protease By similarity
Active sitei457 – 4571For protease activity; shared with dimeric partner By similarity
Sitei578 – 5792Cleavage; by Ty2 protease By similarity
Metal bindingi667 – 6671Magnesium; catalytic; for integrase activity By similarity
Metal bindingi732 – 7321Magnesium; catalytic; for integrase activity By similarity
Sitei1232 – 12332Cleavage; by Ty2 protease By similarity
Metal bindingi1361 – 13611Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1442 – 14421Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1443 – 14431Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi1625 – 16251Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1667 – 16671Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi1700 – 17001Magnesium; 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

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 Ty2-OR1 Gag-Pol polyprotein
Alternative name(s):
TY2A-TY2B
Transposon Ty2 TYA-TYB polyprotein
Cleaved into the following 4 chains:
Capsid protein
Short name:
CA
Ty2 protease (EC:3.4.23.-)
Short name:
PR
Integrase
Short name:
IN
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
Gene namesi
Name:TY2B-OR1
Synonyms:YORCTy2-1 POL
Ordered Locus Names:YOR192C-B
ORF Names:O4785
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

CYGDiYOR192c-b.
SGDiS000007354. YOR192C-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 – 17701770Transposon Ty2-OR1 Gag-Pol polyprotein
PRO_0000279340Add
BLAST
Chaini1 – 397397Capsid protein By similarity
PRO_0000279341Add
BLAST
Chaini398 – 578181Ty2 protease By similarity
PRO_0000279342Add
BLAST
Chaini579 – 1232654Integrase By similarity
PRO_0000279343Add
BLAST
Chaini1233 – 1770538Reverse transcriptase/ribonuclease H By similarity
PRO_0000279344Add
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.

Expressioni

Gene expression databases

GenevestigatoriQ12113.

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

BioGridi34588. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ12113.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini656 – 831176Integrase catalytic
Add
BLAST
Domaini1353 – 1491139Reverse transcriptase Ty1/copia-type
Add
BLAST
Domaini1625 – 1767143RNase H Ty1/copia-type
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni295 – 397103RNA-binding By similarity
Add
BLAST
Regioni579 – 63658Integrase-type zinc finger-like
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1193 – 122735Bipartite 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.
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.

Sequence similaritiesi

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00730000111602.
HOGENOMiHOG000280731.
OMAiPHITESH.
OrthoDBiEOG7TJ3S3.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR025724. GAG-pre-integrase_dom.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamiPF13976. gag_pre-integrs. 1 hit.
PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50994. 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.

Isoform Transposon Ty2-OR1 Gag-Pol polyprotein (identifier: Q12113-1) [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

MESQQLSQNS PTFHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV     50
NSQQETTPGT SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN 100
WAHYQQPSMM TCSHYQTSPA YYQPDPHYPL PQYIPPLSTS SPDPIGSQDQ 150
HSEVPQAKTK VRNNVLPPHT LTSEENFSTW VKFYIRFLKN SNLGDIIPND 200
QGEIKRQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN YSDILTVLCK 250
SVSKMQTNNQ ELKDWIALAN LEYNGSTSAD TFEITVSTII QRLKENNINV 300
SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN 350
LNKPSQYKQH SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA 400
TSSKFSRVNN DHINESTVSS QYLSDDNELS LGQQQKESKP TRTIDSNDEL 450
PDHLLIDSGA SQTLVRSAHY LHHATPNSEI NIVDAQKQDI PINAIGNLHF 500
NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN TLERSDGTVL 550
APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH 600
ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS 650
RLKYQESYEP FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH 700
DRREESILNV FTSILAFIKN QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG 750
ITACYTTTAD SRAHGVAERL NRTLLNDCRT LLHCSGLPNH LWFSAVEFST 800
IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN HNPDSKIHPR 850
GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQNKQT KLDQFDYDTL 900
TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND 950
FSSQSLNPLQ LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE 1000
STEMGGTIES DTTSPRHSST FTARNQKRPG SPNDMIDLTS QDRVNYGLEN 1050
IKTTRLGGTE EPYIQRNSDT NIKYRTTNST PSIDDRSSNS ESTTPIISIE 1100
TKAACDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD SILDDLPLPD 1150
LTHQSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN 1200
ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD 1250
EAITYNKDNK EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN 1300
SMFIFNKKRD GTHKARFVAR GDIQHPDTYD SDMQSNTVHH YALMTSLSIA 1350
LDNDYYITQL DISSAYLYAD IKEELYIRPP PHLGLNDKLL RLRKSLYGLK 1400
QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF VDDMILFSKD 1450
LNANKKIITT LKKQYDTKII NLGEGDNEIQ YDILGLEIKY QRSKYMKLGM 1500
EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE 1550
MQKLIGLASY VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD 1600
TRDKQLIWHK NKPTKPDNKL VAISDASYGN QPYYKSQIGN IFLLNGKVIG 1650
GKSTKASLTC TSTTEAEIHA VSEAIPLLNN LSHLVQELNK KPIIKGLLTD 1700
SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY YIETNKNIAD 1750
VMTKPLPIKT FKLLTNKWIH 1770

Note: Produced by +1 ribosomal frameshifting between codon Leu-431 and Gly-432 of the YOR192C-A ORF.

Length:1,770
Mass (Da):201,984
Last modified:November 1, 1996 - v1
Checksum:i6E4F703E88939D79
GO
Isoform Transposon Ty2-OR1 Gag polyprotein (identifier: Q12439-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q12439.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:438
Mass (Da):49,736
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z75100 Genomic DNA. Translation: CAA99402.1.
Z75101 Genomic DNA. Translation: CAA99404.1.
BK006948 Genomic DNA. Translation: DAA10966.1.
PIRiS70230.
RefSeqiNP_058185.3. NM_001184388.3. [Q12113-1]

Genome annotation databases

EnsemblFungiiYOR192C-B; YOR192C-B; YOR192C-B. [Q12113-1]
GeneIDi854365.
KEGGisce:YOR192C-B.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z75100 Genomic DNA. Translation: CAA99402.1 .
Z75101 Genomic DNA. Translation: CAA99404.1 .
BK006948 Genomic DNA. Translation: DAA10966.1 .
PIRi S70230.
RefSeqi NP_058185.3. NM_001184388.3. [Q12113-1 ]

3D structure databases

ProteinModelPortali Q12113.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34588. 1 interaction.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOR192C-B ; YOR192C-B ; YOR192C-B . [Q12113-1 ]
GeneIDi 854365.
KEGGi sce:YOR192C-B.

Organism-specific databases

CYGDi YOR192c-b.
SGDi S000007354. YOR192C-B.

Phylogenomic databases

GeneTreei ENSGT00730000111602.
HOGENOMi HOG000280731.
OMAi PHITESH.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 976482.

Gene expression databases

Genevestigatori Q12113.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR025724. GAG-pre-integrase_dom.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view ]
Pfami PF13976. gag_pre-integrs. 1 hit.
PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view ]
SUPFAMi SSF53098. SSF53098. 1 hit.
PROSITEi PS50994. INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(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.

Entry informationi

Entry nameiYO21B_YEAST
AccessioniPrimary (citable) accession number: Q12113
Secondary accession number(s): D6W2Q0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: November 1, 1996
Last modified: May 14, 2014
This is version 97 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. Ty2 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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

External Data

Dasty 3

Similar proteinsi