UniProtKB - Q04214 (YM13B_YEAST)
Transposon Ty1-MR1 Gag-Pol polyprotein
TY1B-MR1
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 similarityThe aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.
By similarityReverse 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 similarityIntegrase (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 similarityMiscellaneous
Catalytic activityi
- Endonucleolytic cleavage to 5'-phosphomonoester. EC:3.1.26.4
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 461 | For protease activity; shared with dimeric partnerPROSITE-ProRule annotation | 1 | |
Metal bindingi | 671 | Magnesium 1; catalytic; for integrase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 736 | Magnesium 1; catalytic; for integrase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1346 | Magnesium 2; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1427 | Magnesium 2; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1428 | Magnesium 2; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1610 | Magnesium 3; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1652 | Magnesium 3; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 | |
Metal bindingi | 1685 | Magnesium 3; catalytic; for RNase H activityPROSITE-ProRule annotation | 1 |
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
Keywordsi
Names & Taxonomyi
Protein namesi | Recommended name: Transposon Ty1-MR1 Gag-Pol polyproteinAlternative name(s): Gag-Pol-p199 TY1A-TY1B Transposon Ty1 TYA-TYB polyprotein p190 Cleaved into the following 4 chains: Alternative name(s): Gag-p45 p54 Alternative name(s): Pol-p20 p23 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-MR1 Synonyms:YMRCTy1-3 POL Ordered Locus Names:YMR045C ORF Names:YM9532.10C |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000004648, YMR045C |
VEuPathDBi | FungiDB:YMR045C |
Subcellular locationi
Nucleus
- nucleus Source: SGD
- retrotransposon nucleocapsid Source: SGD
Other locations
- cytoplasm Source: UniProtKB-SubCell
Keywords - Cellular componenti
Cytoplasm, NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000199567 | 1 – 1755 | Transposon Ty1-MR1 Gag-Pol polyproteinAdd BLAST | 1755 | |
ChainiPRO_0000279127 | 1 – 401 | Capsid proteinBy similarityAdd BLAST | 401 | |
ChainiPRO_0000279128 | 402 – 582 | Ty1 proteaseBy similarityAdd BLAST | 181 | |
ChainiPRO_0000279129 | 583 – 1217 | IntegraseBy similarityAdd BLAST | 635 | |
ChainiPRO_0000279130 | 1218 – 1755 | Reverse transcriptase/ribonuclease HBy similarityAdd BLAST | 538 |
Post-translational modificationi
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 401 – 402 | Cleavage; by Ty1 proteaseBy similarity | 2 | |
Sitei | 582 – 583 | Cleavage; by Ty1 proteaseBy similarity | 2 | |
Sitei | 1217 – 1218 | Cleavage; by Ty1 proteaseBy similarity | 2 |
Proteomic databases
PaxDbi | Q04214 |
PTM databases
iPTMneti | Q04214 |
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 similarityProtein-protein interaction databases
BioGRIDi | 35218, 12 interactors |
IntActi | Q04214, 4 interactors |
MINTi | Q04214 |
Miscellaneous databases
RNActi | Q04214, protein |
Structurei
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 660 – 835 | Integrase catalyticPROSITE-ProRule annotationAdd BLAST | 176 | |
Domaini | 1338 – 1476 | Reverse transcriptase Ty1/copia-typeAdd BLAST | 139 | |
Domaini | 1610 – 1752 | RNase H Ty1/copia-typeAdd BLAST | 143 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 1 – 88 | DisorderedSequence analysisAdd BLAST | 88 | |
Regioni | 137 – 174 | DisorderedSequence analysisAdd BLAST | 38 | |
Regioni | 299 – 401 | RNA-bindingBy similarityAdd BLAST | 103 | |
Regioni | 350 – 420 | DisorderedSequence analysisAdd BLAST | 71 | |
Regioni | 583 – 640 | Integrase-type zinc finger-likeAdd BLAST | 58 | |
Regioni | 958 – 1172 | DisorderedSequence analysisAdd BLAST | 215 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 1178 – 1212 | Bipartite nuclear localization signalBy similarityAdd BLAST | 35 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 1 – 67 | Polar residuesSequence analysisAdd BLAST | 67 | |
Compositional biasi | 137 – 173 | Polar residuesSequence analysisAdd BLAST | 37 | |
Compositional biasi | 350 – 375 | Basic and acidic residuesSequence analysisAdd BLAST | 26 | |
Compositional biasi | 376 – 420 | Polar residuesSequence analysisAdd BLAST | 45 | |
Compositional biasi | 969 – 983 | Basic and acidic residuesSequence analysisAdd BLAST | 15 | |
Compositional biasi | 993 – 1015 | Polar residuesSequence analysisAdd BLAST | 23 | |
Compositional biasi | 1040 – 1056 | Basic and acidic residuesSequence analysisAdd BLAST | 17 | |
Compositional biasi | 1057 – 1080 | Polar residuesSequence analysisAdd BLAST | 24 | |
Compositional biasi | 1094 – 1111 | Polar residuesSequence analysisAdd BLAST | 18 | |
Compositional biasi | 1149 – 1172 | Polar residuesSequence analysisAdd BLAST | 24 |
Domaini
Keywords - Domaini
Zinc-fingerPhylogenomic databases
eggNOGi | KOG0017, Eukaryota |
HOGENOMi | CLU_244151_0_0_1 |
InParanoidi | Q04214 |
Family and domain databases
Gene3Di | 3.30.420.10, 1 hit |
InterProi | View protein in InterPro IPR001969, Aspartic_peptidase_AS IPR043502, DNA/RNA_pol_sf IPR001584, Integrase_cat-core IPR012337, RNaseH-like_sf IPR036397, RNaseH_sf IPR013103, RVT_2 IPR015820, TYA |
Pfami | View protein in Pfam PF00665, rve, 1 hit PF07727, RVT_2, 1 hit PF01021, TYA, 1 hit |
SUPFAMi | SSF53098, SSF53098, 1 hit SSF56672, SSF56672, 1 hit |
PROSITEi | View protein in PROSITE PS00141, ASP_PROTEASE, 1 hit PS50994, INTEGRASE, 1 hit |
s (2)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry describes 2 produced by isoformsiribosomal frameshifting. AlignAdd to basketThis isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MESQQLSQHS PISHGSACAS VTSKEVQTTQ DPLDISASKT EECEKVSTQA
60 70 80 90 100
NSQQPTTPLS SAVPENHHHA SPQAAQVPLP QNGPYPQQRM MNTQQANISG
110 120 130 140 150
WPVYGHPSLM PYPPYQMSPM YAPPGAQSQF TQYPQYVGTH LNTPSPESGN
160 170 180 190 200
SFPDSSSAKS NMTSTNQHVR PPPILTSPND FLNWVKIYIK FLQNSNLGDI
210 220 230 240 250
IPTATRKAVR QMTDDELTFL CHTFQLFAPS QFLPPWVKDI LSVDYTDIMK
260 270 280 290 300
ILSKSINKMQ SDTQEVNDIT TLATLHYNGS TPADAFEAEV TNILDRLNNN
310 320 330 340 350
GIPINNKVAC QFIMRGLSGE YKFLRYARHR CIHMTVADLF SDIHSMYEEQ
360 370 380 390 400
QESKRNKSTH RRSPSDEKKD SRTYTNTTKP KSITRNSQKP NNSQSRTARA
410 420 430 440 450
HNVSTFNNSP GPDNDLIRGS TTEPIQLKNT HDLHLGQELT ESTVNHTNHS
460 470 480 490 500
DDKLPGHLLL 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 NRLTASYHSF IASNEIQQSN DLNIESDHDF QSDIELHPEQ
960 970 980 990 1000
LRNVLSKAVS PTDSTPPSTH TEDSKRVSKT NIRAPREVDP NISESNILPS
1010 1020 1030 1040 1050
KKRSSTPQIS DIESTGSGGM HRLDVPLLAP MSQSNTHESS HASKSKDFRH
1060 1070 1080 1090 1100
SDSYSDNETN HTNVPISSTG GTNNKTVPQT SEQETEKRII HRSPSIDTSS
1110 1120 1130 1140 1150
SESNSLHHVV PIKTSDTCPK ENTEESIIAD LPLPDLPPEP PTELSDSFKE
1160 1170 1180 1190 1200
LPPINSRQTN SSLGGIGDSN AYTTINSKKR SLEDNETEIK VSRDTWNTKN
1210 1220 1230 1240 1250
MRSLEPPRSK KRIHLIAAVK AVKSIKPIRT TLRYDEAITY NKDIKEKEKY
1260 1270 1280 1290 1300
IEAYHKEVNQ LLKMKTWDTD KYYDRKEIDP KRVINSMFIF NRKRDGTHKA
1310 1320 1330 1340 1350
RFVARGDIQH PDTYDSGMQS NTVHHYALMT SLSLALDNNY YITQLDISSA
1360 1370 1380 1390 1400
YLYADIKEEL YIRPPPHLGM NDKLIRLKKS LYGLKQSGAN WYETIKSYLI
1410 1420 1430 1440 1450
KQCGMEEVRG WSCVFENSQV TICLFVDDMV LFSKNLNSNK RIIDKLKMQY
1460 1470 1480 1490 1500
DTKIINLGES DEEIQYDILG LEIKYQRGKY MKLGMENSLT EKIPKLNVPL
1510 1520 1530 1540 1550
NPKGRKLSAP GQPGLYIDQQ ELELEEDDYK MKVHEMQKLI GLASYVGYKF
1560 1570 1580 1590 1600
RFDLLYYINT LAQHILFPSK QVLDMTYELI QFIWNTRDKQ LIWHKSKPVK
1610 1620 1630 1640 1650
PTNKLVVISD ASYGNQPYYK SQIGNIYLLN GKVIGGKSTK ASLTCTSTTE
1660 1670 1680 1690 1700
AEIHAISESV PLLNNLSYLI QELDKKPITK GLLTDSKSTI SIIISNNEEK
1710 1720 1730 1740 1750
FRNRFFGTKA MRLRDEVSGN HLHVCYIETK KNIADVMTKP LPIKTFKLLT
NKWIH
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Sequence cautioni
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | Z48502 Genomic DNA Translation: CAA88411.1 Sequence problems. BK006946 Genomic DNA Translation: DAA09944.1 |
PIRi | S40969 S52894 |
RefSeqi | NP_013759.1, NM_001182542.2 [Q04214-1] |
Genome annotation databases
GeneIDi | 855062 |
KEGGi | sce:YMR045C |
Keywords - Coding sequence diversityi
Ribosomal frameshiftingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | Z48502 Genomic DNA Translation: CAA88411.1 Sequence problems. BK006946 Genomic DNA Translation: DAA09944.1 |
PIRi | S40969 S52894 |
RefSeqi | NP_013759.1, NM_001182542.2 [Q04214-1] |
3D structure databases
ModBasei | Search... |
SWISS-MODEL-Workspacei | Submit a new modelling project... |
Protein-protein interaction databases
BioGRIDi | 35218, 12 interactors |
IntActi | Q04214, 4 interactors |
MINTi | Q04214 |
PTM databases
iPTMneti | Q04214 |
Proteomic databases
PaxDbi | Q04214 |
Genome annotation databases
GeneIDi | 855062 |
KEGGi | sce:YMR045C |
Organism-specific databases
SGDi | S000004648, YMR045C |
VEuPathDBi | FungiDB:YMR045C |
Phylogenomic databases
eggNOGi | KOG0017, Eukaryota |
HOGENOMi | CLU_244151_0_0_1 |
InParanoidi | Q04214 |
Miscellaneous databases
RNActi | Q04214, protein |
Family and domain databases
Gene3Di | 3.30.420.10, 1 hit |
InterProi | View protein in InterPro IPR001969, Aspartic_peptidase_AS IPR043502, DNA/RNA_pol_sf IPR001584, Integrase_cat-core IPR012337, RNaseH-like_sf IPR036397, RNaseH_sf IPR013103, RVT_2 IPR015820, TYA |
Pfami | View protein in Pfam PF00665, rve, 1 hit PF07727, RVT_2, 1 hit PF01021, TYA, 1 hit |
SUPFAMi | SSF53098, SSF53098, 1 hit SSF56672, SSF56672, 1 hit |
PROSITEi | View protein in PROSITE PS00141, ASP_PROTEASE, 1 hit PS50994, INTEGRASE, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | YM13B_YEAST | |
Accessioni | Q04214Primary (citable) accession number: Q04214 Secondary accession number(s): D6VZM0 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | November 1, 1997 |
Last sequence update: | March 6, 2007 | |
Last modified: | February 23, 2022 | |
This is version 158 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteome, Transposable elementDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome XIII
Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names