P47024 (YJ41B_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transposon Ty4-J Gag-Pol polyprotein

Alternative name(s):
TY4A-TY4B
Transposon Ty4 TYA-TYB polyprotein

Including the following 4 domains:

1. Capsid protein
   Short name=CA
2. Ty4 protease
   Short name=PR
   EC=3.4.23.-
3. Integrase
   Short name=IN
4. Reverse transcriptase/ribonuclease H
   Short name=RT
   Short name=RT-RH
   EC=2.7.7.49
   EC=2.7.7.7
   EC=3.1.26.4

Gene names

Name:	TY4B-J
Synonyms:	YJLWTy4-1 POL
Ordered Locus Names:	YJL113W
ORF Names:	J0780

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1803 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome 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 activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Endonucleolytic cleavage to 5'-phosphomonoester.
Subunit structure	The protease is a homodimer, whose active site consists of two apposed aspartic acid residues By similarity.
Subcellular location	Cytoplasm. Nucleus By similarity.
Domain	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,D35E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.
Post-translational modification	Proteolytically processed into capsid protein (CA), Ty4 protease (PR), integrase (IN) and reverse transcriptase/ribonuclease H (RT) proteins Probable. 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.
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. Ty4 retrotransposons belong to the copia elements (pseudoviridae).
Sequence similarities	Contains 1 integrase catalytic domain. Contains 1 reverse transcriptase Ty1/copia-type domain. Contains 1 RNase H Ty1/copia-type domain.
Sequence caution	The sequence CAA89409.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence DAA08686.2 differs from that shown. Reason: Frameshift at positions 226 and 240.

Ontologies

Keywords
Biological process	Capsid maturation DNA integration DNA recombination Transposition
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Ribosomal frameshifting
Domain	Coiled coil Zinc-finger
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding RNA-binding Zinc
Molecular function	Aspartyl protease DNA-directed DNA polymerase Endonuclease Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed DNA polymerase Transferase
Technical term	Complete proteome Multifunctional enzyme Reference proteome Transposable element
Gene Ontology (GO)
Biological_process	DNA integration Inferred from electronic annotation. Source: UniProtKB-KW DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transposition, RNA-mediated Inferred from sequence or structural similarity Ref.5. Source: SGD viral procapsid maturation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	mitochondrion Inferred from direct assay PubMed 14576278PubMed 16823961. Source: SGD retrotransposon nucleocapsid Inferred from sequence or structural similarity Ref.5. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from sequence or structural similarity Ref.5. Source: SGD RNA binding Inferred from sequence or structural similarity Ref.5. Source: SGD RNA-directed DNA polymerase activity Inferred from sequence or structural similarity Ref.5. Source: SGD aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW peptidase activity Inferred from sequence or structural similarity Ref.5. Source: SGD ribonuclease H activity Inferred from electronic annotation. Source: EC ribonuclease activity Inferred from sequence or structural similarity Ref.5. Source: SGD zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift.

Isoform Transposon Ty4-J Gag-Pol polyprotein (identifier: P47024-1)

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.

Note: Produced by +1 ribosomal frameshifting between codon Leu-363 and Gly-364 of the YJL114W ORF.

Isoform Transposon Ty4-J Gag polyprotein (identifier: P47023-1)

The sequence of this isoform can be found in the external entry P47023.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1803	1803	Transposon Ty4-J Gag-Pol polyprotein		PRO_0000203502
Regions
	Domain	620 – 787	168	Integrase catalytic
	Domain	1376 – 1511	136	Reverse transcriptase Ty1/copia-type
	Domain	1645 – 1791	147	RNase H Ty1/copia-type
	Region	382 – 502	121	Ty4 protease
	Region	540 – 600	61	Integrase-type zinc finger-like
	Coiled coil	39 – 115	77	Potential
Sites
	Active site	415	1	For protease activity; shared with dimeric partner By similarity
	Metal binding	631	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	696	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	1384	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1463	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1464	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1645	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1687	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1721	1	Magnesium; catalytic; for RNase H activity By similarity
Experimental info
	Sequence conflict	452	1	V → L in X67284. Ref.1
	Sequence conflict	684	1	T → A in X67284. Ref.1
	Sequence conflict	920	1	A → S in X67284. Ref.1
	Sequence conflict	1020	1	S → R in X67284. Ref.1
	Sequence conflict	1803	1	Y → YLINEVLNTQISVEVQ in X67284. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty4-J Gag-Pol polyprotein [UniParc]. Last modified November 2, 2010. Version 3. Checksum: A58D1D4E96F7C9C9	FASTA	1,803	207,710
	10 20 30 40 50 60 MATPVRGETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVRQ YQRNLNRFKT 70 80 90 100 110 120 ILNGLKAEEE KLSEADDIQM LAEKLLKLGE TIDKVENRIV DLVEKIQLLE TNENNNILHE 130 140 150 160 170 180 HIDATGTYYL FDTLTSTNKR FYPKDCVFDY RTNNVENIPI LLNNFKKFIK KYQFDDVFEN 190 200 210 220 230 240 DIIEIDPREN EILCKIIKEG LGESLDIMNT NTTDIFRIID GLKKQNIEVC MVEMSELEPG 250 260 270 280 290 300 EKVLVDTTCR NSALLMNKLQ KLVLMEKWIF SKCCQDCPNL KDYLQEAIMG TLHESLRNSV 310 320 330 340 350 360 KQRLYNIPHD VGIDHEEFLI NTVIETVIDL SPIADDQIEN SCMYCKSVFH CSINCKKKPN 370 380 390 400 410 420 RELGLTRPIS QKPIIYKVHR DNNHLSPVQN EQKSWNKTQK RSNKVYNSKK LVIIDTGSGV 430 440 450 460 470 480 NITNDKTLLH NYEDSNRSTR FFGIGKNSSV SVKGYGYIKI KNGHNNTDNK CLLTYYVPEE 490 500 510 520 530 540 ESTIISCYDL AKKTKMVLSR KYTRLGNKII KIKTKIVNGV IHVKMNELIE RPSDDSKINA 550 560 570 580 590 600 IKPTSSPGFK LNKRSITLED AHKRMGHTGI QQIENSIKHN HYEESLDLIK EPNEFWCQTC 610 620 630 640 650 660 KISKATKRNH YTGSMNNHST DHEPGSSWCM DIFGPVSSSN ADTKRYMLIM VDNNTRYCMT 670 680 690 700 710 720 STHFNKNAET ILAQVRKNIQ YVETQFDRKV REINSDRGTE FTNDQIEEYF ISKGIHHILT 730 740 750 760 770 780 STQDHAANGR AERYIRTIIT DATTLLRQSN LRVKFWEYAV TSATNIRNYL EHKSTGKLPL 790 800 810 820 830 840 KAISRQPVTV RLMSFLPFGE KGIIWNHNHK KLKPSGLPSI ILCKDPNSYG YKFFIPSKNK 850 860 870 880 890 900 IVTSDNYTIP NYTMDGRVRN TQNINKSHQF SSDNDDEEDQ IETVTNLCEA LENYEDDNKP 910 920 930 940 950 960 ITRLEDLFTE EELSQIDSNA KYPSPSNNLE GDLDYVFSDV EESGDYDVES ELSTTNNSIS 970 980 990 1000 1010 1020 TDKNKILSNK DFNSELASTE ISISGIDKKG LINTSHIDED KYDEKVHRIP SIIQEKLVGS 1030 1040 1050 1060 1070 1080 KNTIKINDEN KISDRIRSKN IGSILNTGLS RCVDITDESI TNKDESMHNA KPELIQEQLK 1090 1100 1110 1120 1130 1140 KTNHETSFPK EGSIGTNVKF RNTNNEISLK TGDTSLPIKT LESINNHHSN DYSTNKVEKF 1150 1160 1170 1180 1190 1200 EKENHHPPPI EDIVDMSDQT DMESNCQDGN NLKELKVTDK NVPTDNGTNV SPRLEQNIEA 1210 1220 1230 1240 1250 1260 SGSPVQTVNK SAFLNKEFSS LNMKRKRKRH DKNNSLTSYE LERDKKRSKK NRVKLIPDNM 1270 1280 1290 1300 1310 1320 ETVSAPKIRA IYYNEAISKN PDLKEKHEYK QAYHKELQNL KDMKVFDVDV KYSRSEIPDN 1330 1340 1350 1360 1370 1380 LIVPTNTIFT KKRNGIYKAR IVCRGDTQSP DTYSVITTES LNHNHIKIFL MIANNRNMFM 1390 1400 1410 1420 1430 1440 KTLDINHAFL YAKLEEEIYI PHPHDRRCVV KLNKALYGLK QSPKEWNDHL RQYLNGIGLK 1450 1460 1470 1480 1490 1500 DNSYTPGLYQ TEDKNLMIAV YVDDCVIAAS NEQRLDEFIN KLKSNFELKI TGTLIDDVLD 1510 1520 1530 1540 1550 1560 TDILGMDLVY NKRLGTIDLT LKSFINRMDK KYNEELKKIR KSSIPHMSTY KIDPKKDVLQ 1570 1580 1590 1600 1610 1620 MSEEEFRQGV LKLQQLLGEL NYVRHKCRYD IEFAVKKVAR LVNYPHERVF YMIYKIIQYL 1630 1640 1650 1660 1670 1680 VRYKDIGIHY DRDCNKDKKV IAITDASVGS EYDAQSRIGV ILWYGMNIFN VYSNKSTNRC 1690 1700 1710 1720 1730 1740 VSSTEAELHA IYEGYADSET LKVTLKELGE GDNNDIVMIT DSKPAIQGLN RSYQQPKEKF 1750 1760 1770 1780 1790 1800 TWIKTEIIKE KIKEKSIKLL KITGKGNIAD LLTKPVSASD FKRFIQVLKN KITSQDILAS TDY
	Isoform Transposon Ty4-J Gag polyprotein [UniParc]. See P47023.		–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Ty4, a new retrotransposon from Saccharomyces cerevisiae, flanked by tau-elements." Janetzky B., Lehle L. J. Biol. Chem. 267:19798-19805(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon." Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C. Yeast 12:1471-1474(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X." Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K. , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L. EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 226 AND 240. Strain: ATCC 204508 / S288c.
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X67284 Genomic DNA. No translation available. Z49389 Genomic DNA. Translation: CAA89409.1. Sequence problems. BK006943 Genomic DNA. Translation: DAA08686.2. Frameshift.
PIR	S31262. S56894.
RefSeq	NP_012421.2. NM_001181546.2.
3D structure databases
ProteinModelPortal	P47024.
ModBase	Search...
Protein-protein interaction databases
IntAct	P47024. 6 interactions.
MINT	MINT-436711.
STRING	4932.YJL113W.
Proteomic databases
PaxDb	P47024.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	853330.
KEGG	sce:YJL113W.
Organism-specific databases
SGD	S000003649. YJL113W.
Phylogenomic databases
eggNOG	NOG283194.
HOGENOM	HOG000155565.
OrthoDB	EOG469V3D.
Gene expression databases
ArrayExpress	P47024.
Genevestigator	P47024.
GermOnline	YJL113W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR001584. Integrase_cat-core. IPR012337. RNaseH-like_dom. IPR013103. RVT_2. IPR001878. Znf_CCHC. [Graphical view]
Pfam	PF00665. rve. 1 hit. PF07727. RVT_2. 1 hit. [Graphical view]
SMART	SM00343. ZnF_C2HC. 1 hit. [Graphical view]
SUPFAM	SSF53098. RNaseH_fold. 1 hit.
PROSITE	PS50994. INTEGRASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	973695.

Entry information

Entry name

YJ41B_YEAST

Accession

Primary (citable) accession number: P47024
Secondary accession number(s): D6VW70, P87192

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	November 2, 2010
Last modified:	April 3, 2013
This is version 86 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program