Reviewed, UniProtKB/Swiss-Prot Q12491 (YB21B_YEAST)

Names and origin

Protein names

Recommended name:
    Transposon Ty2-B 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-B
Synonyms:	YBLWTy2-1 POL
Ordered Locus Names:	YBL100W-B
ORF Names:	YBL0822, YBL101W-B

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 further processed into a mature form.
Protein existence	Evidence at protein 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. Nucleus By 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	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 CAA55998.1 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
PTM	Phosphoprotein
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 magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease H activity Inferred from electronic annotation. Source: EC 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 Ty2-B Gag-Pol polyprotein (identifier: Q12491-1)

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-431 and Gly-432 of the YBL100W-A ORF.

Isoform Transposon Ty2-B Gag polyprotein (identifier: Q12260-1)

The sequence of this isoform can be found in the external entry Q12260-1.
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 – 1770	1770	Transposon Ty2-B Gag-Pol polyprotein		PRO_0000279270
	Chain	1 – 397	397	Capsid protein By similarity		PRO_0000279271
	Chain	398 – 578	181	Ty2 protease By similarity		PRO_0000279272
	Chain	579 – 1232	654	Integrase By similarity		PRO_0000279273
	Chain	1233 – 1770	538	Reverse transcriptase/ribonuclease H By similarity		PRO_0000279274
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
Amino acid modifications
	Modified residue	987	1	Phosphoserine Ref.5
	Modified residue	993	1	Phosphothreonine Ref.5
	Modified residue	1014	1	Phosphoserine Ref.5
	Modified residue	1031	1	Phosphoserine Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty2-B Gag-Pol polyprotein [UniParc]. Last modified November 1, 1996. Version 1. Checksum: EAE87178C187B31B	FASTA	1,770	202,215
	10 20 30 40 50 60 MESQQLHQNP HSLHGSAYAS VTSKEVSSNQ DPLAVSASNL PEFDRDSTKV NSQQETTPGT 70 80 90 100 110 120 SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN WAHYQQPSMM TCSHYQTSPA 130 140 150 160 170 180 YYQPDPHYPL PQYIPPLSTS SPDPIDSQDQ HSEVPQAKTK VRNNVLPPHT LTSEENFYTW 190 200 210 220 230 240 VKFYIRFLKN SNLGDIIPND QGEIKRQMTY 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 NYVILQDNQS KLDQFNYDTL 910 920 930 940 950 960 TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND FSSQSMNPLQ 970 980 990 1000 1010 1020 LDHEPVQKVR ALKEVDADIS EYNILPSPVR SRTPHIINKE STEMGGTIES DTTSPRHSST 1030 1040 1050 1060 1070 1080 FTARNQKRPG SPNDMIDLTS QDRVNYELEN IKTTRLGGTE EPYIQRNSDT NIKYRTTNST 1090 1100 1110 1120 1130 1140 PSIDDRSPDS DSTTPIISIE TKAACDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD 1150 1160 1170 1180 1190 1200 SILDDLPLPD LTNKSPTDTS DVSKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN 1210 1220 1230 1240 1250 1260 ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD EAITYNEDNK 1270 1280 1290 1300 1310 1320 EKDRYIEAYH KEINQLLRMN 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 LNANEKIITT LKKQYDTKII NLGESDNEIQ YDILGLEIKY QRSKYMKLGM 1510 1520 1530 1540 1550 1560 EKSLTEKLPK LNVPLNPKGK KLSAPGQPGH 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
	Isoform Transposon Ty2-B Gag polyprotein. See Q12260.	FASTA	–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence analysis of a 78.6 kb segment of the left end of Saccharomyces cerevisiae chromosome II." Obermaier B., Gassenhuber J., Piravandi E., Domdey H. Yeast 11:1103-1112(1995) [PubMed: 7502586] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed: 7813418] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[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.
[5]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-987; THR-993; SER-1014 AND SER-1031, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X79489 Genomic DNA. Translation: CAA55998.1. Sequence problems. Z35861 Genomic DNA. Translation: CAA84922.1. Z35862 Genomic DNA. Translation: CAA84927.2.
PIR	S45842.
RefSeq	NP_009450.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q12491.
Genome annotation databases
Ensembl	YBL100W-B; YBL100W-B; YBL100W-B; Saccharomyces cerevisiae. [Genome view]
GeneID	852175.
KEGG	sce:YBL100W-B.
Organism-specific databases
CYGD	YBL100w-b.
SGD	S000002149. YBL100W-B.
Phylogenomic databases
HOGENOM	HBG204407.
OMA	RAGHEIL.
OrthoDB	EOG9869VW.
Enzyme and pathway databases
BRENDA	2.7.7.49. 250. 2.7.7.7. 250. 3.1.26.4. 250.
Gene expression databases
Genevestigator	Q12491.
Family and domain databases
InterPro	IPR001584. Integrase_cat-core. IPR012337. PolynucTfrase_RNaseH_fold. 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]
PROSITE	PS50994. INTEGRASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	970632.

Entry information

Entry name

YB21B_YEAST

Accession

Primary (citable) accession number: Q12491
Secondary accession number(s): Q05679

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	November 1, 1996
Last modified:	December 15, 2009
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)