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Protein

Transposon Ty2-OR1 Gag-Pol polyprotein

Gene

TY2B-OR1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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).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)DescriptionActionsGraphical viewLength
Active sitei457For protease activity; shared with dimeric partnerBy similarity1
Metal bindingi667Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi732Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1361Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1442Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1443Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1625Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1667Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1700Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1

GO - Molecular functioni

  • aspartic-type endopeptidase activity Source: UniProtKB-KW
  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • peptidase activity Source: SGD
  • ribonuclease activity Source: SGD
  • RNA binding Source: SGD
  • RNA-directed DNA polymerase activity Source: SGD
  • RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

GO - Biological processi

  • DNA integration Source: UniProtKB-KW
  • DNA recombination Source: UniProtKB-KW
  • transposition, RNA-mediated Source: SGD
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
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR192C-B.
SGDiS000007354. YOR192C-B.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
  • retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002793401 – 1770Transposon Ty2-OR1 Gag-Pol polyproteinAdd BLAST1770
ChainiPRO_00002793411 – 397Capsid proteinBy similarityAdd BLAST397
ChainiPRO_0000279342398 – 578Ty2 proteaseBy similarityAdd BLAST181
ChainiPRO_0000279343579 – 1232IntegraseBy similarityAdd BLAST654
ChainiPRO_00002793441233 – 1770Reverse transcriptase/ribonuclease HBy similarityAdd BLAST538

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei397 – 398Cleavage; by Ty2 proteaseBy similarity2
Sitei578 – 579Cleavage; by Ty2 proteaseBy similarity2
Sitei1232 – 1233Cleavage; by Ty2 proteaseBy similarity2

Proteomic databases

PRIDEiQ12113.

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

Structurei

3D structure databases

ProteinModelPortaliQ12113.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini656 – 831Integrase catalyticPROSITE-ProRule annotationAdd BLAST176
Domaini1353 – 1491Reverse transcriptase Ty1/copia-typeAdd BLAST139
Domaini1625 – 1767RNase H Ty1/copia-typeAdd BLAST143

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni295 – 397RNA-bindingBy similarityAdd BLAST103
Regioni579 – 636Integrase-type zinc finger-likeAdd BLAST58

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1193 – 1227Bipartite nuclear localization signalBy similarityAdd BLAST35

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

GeneTreeiENSGT00860000133955.
HOGENOMiHOG000280731.
InParanoidiQ12113.
OrthoDBiEOG092C2F0T.

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. AlignAdd to basket

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

        10         20         30         40         50
MESQQLSQNS PTFHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV
60 70 80 90 100
NSQQETTPGT SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN
110 120 130 140 150
WAHYQQPSMM TCSHYQTSPA YYQPDPHYPL PQYIPPLSTS SPDPIGSQDQ
160 170 180 190 200
HSEVPQAKTK VRNNVLPPHT LTSEENFSTW VKFYIRFLKN SNLGDIIPND
210 220 230 240 250
QGEIKRQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN YSDILTVLCK
260 270 280 290 300
SVSKMQTNNQ ELKDWIALAN LEYNGSTSAD TFEITVSTII QRLKENNINV
310 320 330 340 350
SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN
360 370 380 390 400
LNKPSQYKQH SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA
410 420 430 440 450
TSSKFSRVNN DHINESTVSS QYLSDDNELS LGQQQKESKP TRTIDSNDEL
460 470 480 490 500
PDHLLIDSGA SQTLVRSAHY LHHATPNSEI NIVDAQKQDI PINAIGNLHF
510 520 530 540 550
NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN TLERSDGTVL
560 570 580 590 600
APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH
610 620 630 640 650
ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS
660 670 680 690 700
RLKYQESYEP FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH
710 720 730 740 750
DRREESILNV FTSILAFIKN QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG
760 770 780 790 800
ITACYTTTAD SRAHGVAERL NRTLLNDCRT LLHCSGLPNH LWFSAVEFST
810 820 830 840 850
IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN HNPDSKIHPR
860 870 880 890 900
GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQNKQT KLDQFDYDTL
910 920 930 940 950
TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND
960 970 980 990 1000
FSSQSLNPLQ LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE
1010 1020 1030 1040 1050
STEMGGTIES DTTSPRHSST FTARNQKRPG SPNDMIDLTS QDRVNYGLEN
1060 1070 1080 1090 1100
IKTTRLGGTE EPYIQRNSDT NIKYRTTNST PSIDDRSSNS ESTTPIISIE
1110 1120 1130 1140 1150
TKAACDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD SILDDLPLPD
1160 1170 1180 1190 1200
LTHQSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN
1210 1220 1230 1240 1250
ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD
1260 1270 1280 1290 1300
EAITYNKDNK EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN
1310 1320 1330 1340 1350
SMFIFNKKRD GTHKARFVAR GDIQHPDTYD SDMQSNTVHH YALMTSLSIA
1360 1370 1380 1390 1400
LDNDYYITQL DISSAYLYAD IKEELYIRPP PHLGLNDKLL RLRKSLYGLK
1410 1420 1430 1440 1450
QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF VDDMILFSKD
1460 1470 1480 1490 1500
LNANKKIITT LKKQYDTKII NLGEGDNEIQ YDILGLEIKY QRSKYMKLGM
1510 1520 1530 1540 1550
EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE
1560 1570 1580 1590 1600
MQKLIGLASY VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD
1610 1620 1630 1640 1650
TRDKQLIWHK NKPTKPDNKL VAISDASYGN QPYYKSQIGN IFLLNGKVIG
1660 1670 1680 1690 1700
GKSTKASLTC TSTTEAEIHA VSEAIPLLNN LSHLVQELNK KPIIKGLLTD
1710 1720 1730 1740 1750
SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY YIETNKNIAD
1760 1770
VMTKPLPIKT FKLLTNKWIH
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:
EMBLi
GenBanki
DDBJi
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_001184388.4. [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:
EMBLi
GenBanki
DDBJi
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_001184388.4. [Q12113-1]

3D structure databases

ProteinModelPortaliQ12113.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ12113.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YOR192C-B.
SGDiS000007354. YOR192C-B.

Phylogenomic databases

GeneTreeiENSGT00860000133955.
HOGENOMiHOG000280731.
InParanoidiQ12113.
OrthoDBiEOG092C2F0T.

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]
ProtoNetiSearch...

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: November 30, 2016
This is version 112 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.