Reviewed, UniProtKB/Swiss-Prot Q12503 (YF21B_YEAST)

Names and origin

Protein names

Recommended name:
    Transposon Ty2-F/Ty2-GR2 Gag-Pol polyprotein
Alternative name(s):
    Transposon Ty2 TYA-TYB polyprotein
    TY2A-TY2B
Cleaved into the following 4 chains:
    1- Recommended name:
            Capsid protein
                Short name=CA
    2- Recommended name:
            Ty2 protease
                Short name=PR
              EC=3.4.23.-
    3- Recommended name:
            Integrase
                Short name=IN
    4- Recommended name:
            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:	TY2B-F
Synonyms:	YFLWTy2-1 POL
Ordered Locus Names:	YFL002W-A
ORF Names:	FN01
AND
Name:	TY2B-GR2
Synonyms:	YGRWTy2-2 POL
Ordered Locus Names:	YGR161W-B
ORF Names:	G7017

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	1770 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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. 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 activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Endonucleolytic cleavage to 5'-phosphomonoester.
Subunit structure	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.
Subcellular location	Cytoplasm. NucleusBy similarity.
Domain	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.
Post-translational modification	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	The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift between the codons for Leu-431 and Gly-432. The Gag polyprotein is also produced by itself from conventional translation of the YFL002W-B and YGR161W-A ORFs. 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).
Sequence similarities	Contains 1 integrase catalytic domain. Contains 1 peptidase A11 domain. Contains 1 reverse transcriptase Ty1/copia-type domain. Contains 1 RNase H Ty1/copia-type domain.
Sequence caution	The sequence BAA09237.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Capsid maturation DNA integration DNA recombination Transposition
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Ribosomal frameshifting
Domain	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)
None. [Check GOA]

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Chain	1 – 1770	1770	Transposon Ty2-F/Ty2-GR2 Gag-Pol polyprotein
	Chain	1 – 397	397	Capsid protein By similarity
	Chain	398 – 578	181	Ty2 protease By similarity
	Chain	579 – 1232	654	Integrase By similarity
	Chain	1233 – 1770	538	Reverse transcriptase/ribonuclease H By similarity
Regions
	Domain	656 – 831	176	Integrase catalytic
	Domain	1353 – 1491	139	Reverse transcriptase Ty1/copia-type
	Domain	1625 – 1767	143	RNase H Ty1/copia-type
	Region	295 – 397	103	RNA-binding By similarity
	Region	579 – 636	58	Integrase-type zinc finger-like
	Motif	1193 – 1227	35	Bipartite nuclear localization signal By similarity
Sites
	Active site	457	1	For protease activity; shared with dimeric partner By similarity
	Metal binding	667	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	732	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	1361	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1442	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1443	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1625	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1667	1	Magnesium; catalytic; for RNase H activity By similarity
	Metal binding	1700	1	Magnesium; catalytic; for RNase H activity By similarity
	Site	397 – 398	2	Cleavage; by Ty2 protease By similarity
	Site	578 – 579	2	Cleavage; by Ty2 protease By similarity
	Site	1232 – 1233	2	Cleavage; by Ty2 protease By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q12503-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 97C0C8F7D431D731	FASTA	1,770	202,039
	10 20 30 40 50 60 MESQQLHQNP HSLHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV NSQQETTPGT 70 80 90 100 110 120 SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN WAHYQQPSMM TCSHYQTSPA 130 140 150 160 170 180 YYQPDPHYPL PQYIPPLSTS SPDPIDSQNQ HSEVPQAETK VRNNVLPPHT LTSEENFSTW 190 200 210 220 230 240 VKFYIRFLKN SNLGDIIPND QGEIKSQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN 250 260 270 280 290 300 YADILTVLCK SVSKMQTNNQ ELKDWIALAN LEYDGSTSAD TFEITVSTII QRLKENNINV 310 320 330 340 350 360 SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN LNKPSQYKQH 370 380 390 400 410 420 SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA TSSKFSRVNN DHINESTVSS 430 440 450 460 470 480 QYLSDDNELS LGQQQKESKP THTIDSNDEL PDHLLIDSGA SQTLVRSAHY LHHATPNSEI 490 500 510 520 530 540 NIVDAQKQDI PINAIGNLHF NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN 550 560 570 580 590 600 TLERSDGTVL APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH 610 620 630 640 650 660 ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS RLKYQESYEP 670 680 690 700 710 720 FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH DRREESILNV FTSILAFIKN 730 740 750 760 770 780 QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG ITACYTTTAD SRAHGVAERL NRTLLNDCRT 790 800 810 820 830 840 LLHCSGLPNH LWFSAVEFST IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN 850 860 870 880 890 900 HNPDSKIHPR GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQDKQS KLDQFNYDTL 910 920 930 940 950 960 TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND FSSQSINPLQ 970 980 990 1000 1010 1020 LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE STEMGGTVES DTTSPRHSST 1030 1040 1050 1060 1070 1080 FTARNQNRPG STNEMIDLTS QDRVNYGLEN IKTTRLGGTE EPYIQRNSDT NIKYRTTNST 1090 1100 1110 1120 1130 1140 PSIDDRSSNS ESTTPIISIE TKAVCDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD 1150 1160 1170 1180 1190 1200 SILDDLPLPD LTHKSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN 1210 1220 1230 1240 1250 1260 ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD EAITYNKDNK 1270 1280 1290 1300 1310 1320 EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN SMFIFNKKRD GTHKARFVAR 1330 1340 1350 1360 1370 1380 GDIQHPDTYD SDMQSNTVHH YALMTSLSIA LDNDYYITQL DISSAYLYAD IKEELYIRPP 1390 1400 1410 1420 1430 1440 PHLGLNDKLL RLRKSLYGLK QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF 1450 1460 1470 1480 1490 1500 VDDMILFSKD LNANKKIITT LKKQYDTKII NLGESDNEIQ YDILGLEIKY QRSKYMKLGM 1510 1520 1530 1540 1550 1560 EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE MQKLIGLASY 1570 1580 1590 1600 1610 1620 VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD TRDKQLIWHK NKPTKPDNKL 1630 1640 1650 1660 1670 1680 VAISDASYGN QPYYKSQIGN IFLLNGKVIG GKSTKASLTC TSTTEAEIHA VSEAIPLLNN 1690 1700 1710 1720 1730 1740 LSHLVQELNK KPIIKGLLTD SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY 1750 1760 1770 YIETKKNIAD VMTKPLPIKT FKLLTNKWIH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae." Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T. Nat. Genet. 10:261-268(1995) [PubMed: 7670463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (YFL002W-A). Strain: ATCC 204511 / S288c / AB972.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (YGR161W-B). Strain: ATCC 96604 / S288c / FY1679.
[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: 9582191] [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: 16093660] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBLGenBankDDBJ	D50617 Genomic DNA. Translation: BAA09237.1. Sequence problems. Z72946 Genomic DNA. Translation: CAA97177.1. Z72947 Genomic DNA. Translation: CAA97186.1.
PIR	S58651.
RefSeq	NP_058163.1. NP_116653.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:8976N.
IntAct	Q12503.
Genome annotation databases
Ensembl	YFL002W-A. Saccharomyces cerevisiae. [Contig view] YGR161W-B. Saccharomyces cerevisiae. [Contig view]
GeneID	850548. 853067.
KEGG	sce:YFL002W-A. sce:YGR161W-B.
Organism-specific databases
CYGD	YFL002w-a. YGR161w-b.
SGD	S000002962. YFL002W-A. S000007370. YGR161W-B.
Phylogenomic databases
HOGENOM	Q12503.
Gene expression databases
ArrayExpress	Q12503.
Family and domain databases
InterPro	IPR001584. Integrase_cat-core. IPR015820. Retrotransposon_Ty1A_N. IPR013103. RVT_2. [Graphical view]
Pfam	PF00665. rve. 1 hit. PF07727. RVT_2. 1 hit. PF01021. TYA. 1 hit. [Graphical view]
ProDom	PD001086. Pept_A11B_Ty1. 1 hit. [Graphical view] [Entries sharing at least one domain]
PROSITE	PS50994. INTEGRASE. 1 hit. [Graphical view]
BLOCKS	Search...
Other Resources
LinkHub	Q12503.
ProtoNet	Search...

Entry information

Entry name

YF21B_YEAST

Accession

Primary (citable) accession number: Q12503
Secondary accession number(s): Q05369

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	November 1, 1996
Last modified:	September 2, 2008
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)