Reviewed, UniProtKB/Swiss-Prot P0C2J7 (YH41B_YEAST)

Names and origin

Protein names

Recommended name:
    Transposon Ty4-H Gag-Pol polyprotein
Alternative name(s):
    Transposon Ty4 TYA-TYB polyprotein
    TY4A-TY4B

Gene names

Name:	TY4B-H
Synonyms:	YHLWTy4-1 POL
Ordered Locus Names:	YHL009W-B
ORF Names:	YHL008W-A

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	1802 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

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.
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,D(35)E 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.

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 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 transposition Inferred from electronic annotation. Source: UniProtKB-KW viral procapsid maturation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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 electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
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-H Gag-Pol polyprotein (identifier: P0C2J7-1)

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-362 and Gly-363 of the YHL009W-A ORF.

Isoform Transposon Ty4-H Gag polyprotein (identifier: Q6Q5P6-1)

The sequence of this isoform can be found in the external entry Q6Q5P6-1.
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 – 1802	1802	Transposon Ty4-H Gag-Pol polyprotein		PRO_0000279380
Regions
	Domain	619 – 786	168	Integrase catalytic
	Domain	1375 – 1510	136	Reverse transcriptase Ty1/copia-type
	Domain	1644 – 1790	147	RNase H Ty1/copia-type
	Region	381 – 501	121	Ty4 protease
	Region	539 – 599	61	Integrase-type zinc finger-like
	Coiled coil	39 – 115	77	Potential
Sites
	Active site	414	1	For protease activity; shared with dimeric partner By similarity
	Metal binding	630	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	695	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	1383	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1462	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1463	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1644	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1686	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1720	1	Magnesium; catalytic; for RNase H activity By similarity

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty4-H Gag-Pol polyprotein [UniParc]. Last modified March 6, 2007. Version 1. Checksum: 7F6A8A3483966588	FASTA	1,802	207,970
	10 20 30 40 50 60 MATPVRDETR NVIDDNISAR IQSKVKTNDT VRQTPSSLRK VSIKDEQVKQ YQRNLNRFKT 70 80 90 100 110 120 ILNGLKAEEE KLSETDDIQM 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 GLKNKYRSLH GRDVRIRAWE 250 260 270 280 290 300 KVLVDTTCRN SALLMNKLQK LVLMEKWIFS KCCQDCPNLK DYLQEAIMGT LHESLRNSVK 310 320 330 340 350 360 QRLYNIPHNV GINHEEFLIN TVIETVIDLS PIADDQIENS CMYCKSVFHC SINCKKKPNR 370 380 390 400 410 420 ELGLTRPISQ KPIIYKVHRD NNNLSPVQNE QKSWNKTQKK SNKVYNSKKL VIIDTGSGVN 430 440 450 460 470 480 ITNDKTLLHN YEDSNRSTRF FGIGKNSSVS VKGYGYIKIK NGHNNTDNKC LLTYYVPEEE 490 500 510 520 530 540 STIISCYDLA KKTKMVLSRK YTRLGNKIIK IKTKIVNGVI HVKMNELIER PSDDSKINAI 550 560 570 580 590 600 KPTSSPGFKL NKRSITLEDA HKRMGHTGIQ QIENSIKHNH YEESLDLIKE PNEFWCQTCK 610 620 630 640 650 660 ISKATKRNHY TGSMNNHSTD HEPGSSWCMD IFGPVSSSNA DTKRYMLIMV DNNTRYCMTS 670 680 690 700 710 720 THFNKNAETI LAQIRKNIQY VETQFDRKVR EINSDRGTEF TNDQIEEYFI SKGIHHILTS 730 740 750 760 770 780 TQDHAANGRA ERYIRTIVTD ATTLLRQSNL RVKFWEYAVT SATNIRNCLE HKSTGKLPLK 790 800 810 820 830 840 AISRQPVTVR LMSFLPFGEK GIIWNHNHKK LKPSGLPSII LCKDPNSYGY KFFIPSKNKI 850 860 870 880 890 900 VTSDNYTIPN YTMDGRVRNT QNIYKSHQFS SHNDNEEDQI ETVTNLCEAL ENYEDDNKPI 910 920 930 940 950 960 TRLEDLFTEE ELSQIDSNAK YPSPSNNLEG DLDYVFSDVE ESGDYDVESE LSTTNTSIST 970 980 990 1000 1010 1020 DKNKILSNKD FNSELASTEI SISEIDKKGL INTSHIDEDK YDEKVHRIPS IIQEKLVGSK 1030 1040 1050 1060 1070 1080 NTIKINDENR ISDRIRSKNI GSILNTGLSR CVDITDESIT NKDESMHNAK PELIQEQFNK 1090 1100 1110 1120 1130 1140 TNHETSFPKE GSIGTNVKFR NTDNEISLKT GDTSLPIKTL ESINNHHSND YSTNKVEKFE 1150 1160 1170 1180 1190 1200 KENHHPPPIE DIVDMSDQTD MESNCQDGNN LKELKVTDKN VPTDNGTNVS PRLEQNIEAS 1210 1220 1230 1240 1250 1260 GSPVQTVNKS AFLNKEFSSL NMKRKRKRHD KNNSLTSYEL ERDKKRSKRN RVKLIPDNME 1270 1280 1290 1300 1310 1320 TVSAQKIRAI YYNEAISKNP DLKEKHEYKQ AYHKELQNLK DMKVFDVDVK YSRSEIPDNL 1330 1340 1350 1360 1370 1380 IVPTNTIFTK KRNGIYKARI VCRGDTQSPD TYSVITTESL NHNHIKIFLM IANNRNMFMK 1390 1400 1410 1420 1430 1440 TLDINHAFLY AKLEEEIYIP HPHDRRCVVK LNKALYGLKQ SPKEWNDHLR QYLNGIGLKD 1450 1460 1470 1480 1490 1500 NSYTPGLYQT EDKNLMIAVY VDDCVIAASN EQRLDEFINK LKSNFELKIT GTLIDDVLDT 1510 1520 1530 1540 1550 1560 DILGMDLVYN KRLGTIDLTL KSFINRMDKK YNEELKKIRK SSIPHMSTYK IDPKKDVLQM 1570 1580 1590 1600 1610 1620 SEEEFRQGVL KLQQLLGELN YVRHKCRYDI NFAVKKVARL VNYPHERVFY MIYKIIQYLV 1630 1640 1650 1660 1670 1680 RYKDIGIHYD RDCNKDKKVI AITDASVGSE YDAQSRIGVI LWYGMNIFNV YSNKSTNRCV 1690 1700 1710 1720 1730 1740 SSTEAELHAI YEGYADSETL KVTLKELGEG DNNDIVMITD SKPAIQGLNR SYQQPKEKFT 1750 1760 1770 1780 1790 1800 WIKTEIIKEK IKEKSIKLLK ITGKGNIADL LTKPVSASDF KRFIQVLKNK ITSQDILAST DY
	Isoform Transposon Ty4-H Gag polyprotein. See Q6Q5P6.	FASTA	–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed: 8091229] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	"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: 9582191] [Abstract] Cited for: NOMENCLATURE.
[3]	"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: 16093660] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBLGenBankDDBJ	U11581 Genomic DNA. No translation available.
PIR	S52611.
RefSeq	NP_058133.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	P0C2J7.
Genome annotation databases
Ensembl	YHL009W-B; YHL009W-B; YHL009W-B; Saccharomyces cerevisiae. [Genome view]
GeneID	856380.
KEGG	sce:YHL009W-B.
NMPDR	fig|4932.3.peg.2995.
Organism-specific databases
CYGD	YHL009w-b.
SGD	S000007372. YHL009W-B.
Phylogenomic databases
OrthoDB	EOG9869VW
Gene expression databases
Genevestigator	P0C2J7.
Family and domain databases
InterPro	IPR001584. Integrase_cat-core. IPR012337. PolynucTfrase_RNaseH_fold. 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]
PROSITE	PS50994. INTEGRASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	981875.

Entry information

Entry name

YH41B_YEAST

Accession

Primary (citable) accession number: P0C2J7

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	March 6, 2007
Last modified:	November 24, 2009
This is version 24 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)