Q7LHG5 (YI31B_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transposon Ty3-I Gag-Pol polyprotein

Alternative name(s):
Gag3-Pol3
Transposon Ty3-2 TYA-TYB polyprotein

Cleaved into the following 8 chains:

1. Capsid protein
   Short name=CA
   Alternative name(s):
   p24
2. Spacer peptide p3
3. Nucleocapsid protein p11
   Short name=NC
4. Ty3 protease
   Short name=PR
   EC=3.4.23.-
   Alternative name(s):
   p16
5. Spacer peptide J
6. 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
   Alternative name(s):
   p55
7. Integrase p52
   Short name=IN
8. Integrase p49
   Short name=IN

Gene names

Name:	TY3B-I
Synonyms:	YILWTy3-1 POL
Ordered Locus Names:	YIL082W-A

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	1498 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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 genomic RNA-nucleocapsid complex By similarity. Ref.4 Nucleocapsid protein p11 (NC) forms the nucleocore that coats the retro-elements dimeric RNA. Binds these RNAs through its zinc fingers By similarity. Promotes primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty3 RNA and initiation of reverse transcription By similarity. Ref.4 The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP By similarity. Ref.4 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. Ref.4 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. Ref.4
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	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. Ty3 retrotransposons belong to the gypsy-like elements (metaviridae). In contrast to Ty3-1 (Ty3-G), Ty3-2 (Ty3-I) is a transpositionally inactive element. The Ty3-2 ORF is truncated by the deletion of a single nucleotide, which causes a frameshift mutation when compared with Ty3-1.
Sequence similarities	Contains 1 CCHC-type zinc finger. Contains 1 integrase catalytic domain. Contains 1 peptidase A2 domain. Contains 1 reverse transcriptase domain. Contains 1 RNase H Ty3/gyspy-type domain.
Sequence caution	The sequence AAA35184.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence CAA86713.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence DAA08470.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Capsid maturation DNA integration DNA recombination
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 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 RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro 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	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell 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 Ty3-I Gag-Pol polyprotein (identifier: Q7LHG5-1)

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 Ala-285 and Val-286 of the YIL082W ORF.

Isoform Transposon Ty3-I Gag polyprotein (identifier: Q99219-1)

The sequence of this isoform can be found in the external entry Q99219.
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
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 1498	1497	Transposon Ty3-I Gag-Pol polyprotein		PRO_0000279367
	Chain	2 – 207	206	Capsid protein		PRO_0000279368
	Peptide	208 – 233	26	Spacer peptide p3		PRO_0000279369
	Chain	234 – 309	76	Nucleocapsid protein p11		PRO_0000279370
	Chain	310 – 442	133	Ty3 protease		PRO_0000279371
	Peptide	443 – 561	119	Spacer peptide J Potential		PRO_0000279372
	Chain	562 – 1037	476	Reverse transcriptase/ribonuclease H		PRO_0000279373
	Chain	1038 – 1498	461	Integrase p52		PRO_0000279374
	Chain	1064 – 1498	435	Integrase p49		PRO_0000279375
Regions
	Domain	646 – 823	178	Reverse transcriptase
	Domain	919 – 1037	119	RNase H Ty3/gyspy-type
	Domain	1185 – 1350	166	Integrase catalytic
	Zinc finger	265 – 282	18	CCHC-type
	Region	1132 – 1171	40	Integrase-type zinc finger-like
Sites
	Active site	336	1	For protease activity; shared with dimeric partner By similarity
	Metal binding	712	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	774	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	775	1	Magnesium; catalytic; for reverse transcriptase activity By similarity
	Metal binding	1201	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	1262	1	Magnesium; catalytic; for integrase activity By similarity
	Site	207 – 208	2	Cleavage; by Ty3 protease
	Site	233 – 234	2	Cleavage; by Ty3 protease
	Site	309 – 310	2	Cleavage; by Ty3 protease
	Site	442 – 443	2	Cleavage; by Ty3 protease Potential
	Site	561 – 562	2	Cleavage; by Ty3 protease
	Site	1037 – 1038	2	Cleavage; by Ty3 protease
	Site	1063 – 1064	2	Cleavage; by Ty3 protease; partial
Experimental info
	Sequence conflict	502	1	G → A in AAA35184. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty3-I Gag-Pol polyprotein [UniParc]. Last modified March 6, 2007. Version 2. Checksum: 4E51C3EFBDEFD7E4	FASTA	1,498	172,369
	10 20 30 40 50 60 MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND 70 80 90 100 110 120 ASRIVYCRRH LLNPAAQWAN DFVQEQGILE ITFDTFIQGL YQHFYKPPDI NKIFNAITQL 130 140 150 160 170 180 SEAKLGIERL NQRFRKIWDR MPPDFMTEKA AIMTYTRLLT KETYNIVRMH KPETLKDAME 190 200 210 220 230 240 EAYQTTALTE RFFPGFELDA DGDTIIGATT HLQEEYDSDY DSEDNLTQNR YVHTVRTRRS 250 260 270 280 290 300 YNKPMSNHRN RRNNNASREE CIKNRLCFYC KKEGHRLNEC RARKAVLTDL ELESKDQQTL 310 320 330 340 350 360 FIKTLPIVHY IAIPEMDNTA EKTIKIQNTK VKTLFDSGSP TSFIRRDIVE LLKYEIYETP 370 380 390 400 410 420 PLRFRGFVAT KSAVTSEAVT IDLKINDLQI TLAAYILDNM DYQLLIGNPI LRRYPKILHT 430 440 450 460 470 480 VLNTRESPDS LKPKTYRSET VNNVRTYSAG NRGNPRNIKL SFAPTILEAT DPKSAGNRGN 490 500 510 520 530 540 PRNTKLSLAP TILEATDPKS AGNRGDSRTK TLSLATTTPA AIDPLTTLDN PGSTQSTFAQ 550 560 570 580 590 600 FPIPEEASIL EEDGKYSNVV STIQSVEPNA TDHSNKDTFC TLPVWLQQKY REIIRNDLPP 610 620 630 640 650 660 RPADINNIPV KHDIEIKPGA RLPRLQPYHV TEKNEQEINK IVQKLLDNKF IVPSKSPCSS 670 680 690 700 710 720 PVVLVPKKDG TFRLCVDYRT LNKATISDPF PLPRIDNLLS RIGNAQIFTT LDLHSGYHQI 730 740 750 760 770 780 PMEPKDRYKT AFVTPSGKYE YTVMPFGLVN APSTFARYMA DTFRDLRFVN VYLDDILIFS 790 800 810 820 830 840 ESPEEHWKHL DTVLERLKNE NLIVKKKKCK FASEETEFLG YSIGIQKIAP LQHKCAAIRD 850 860 870 880 890 900 FPTPKTVKQA QRFLGMINYY RRFIPNCSKI AQPIQLFICD KSQWTEKQDK AIEKLKAALC 910 920 930 940 950 960 NSPVLVPFNN KANYRLTTDA SKDGIGAVLE EVDNKNKLVG VVGYFSKSLE SAQKNYPAGE 970 980 990 1000 1010 1020 LELLGIIKAL HHFRYMLHGK HFTLRTDHIS LLSLQNKNEP ARRVQRWLDD LATYDFTLEY 1030 1040 1050 1060 1070 1080 LAGPKNVVAD AISRAIYTIT PETSRPIDTE SWKSYYKSDP LCSAVLIHMK ELTQHNVTPE 1090 1100 1110 1120 1130 1140 DMSAFRSYQK KLELSETFRK NYSLEDEMIY YQDRLVVPIK QQNAVMRLYH DHTLFGGHFG 1150 1160 1170 1180 1190 1200 VTVTLAKISP IYYWPKLQHS IIQYIRTCVQ CQLIKSHRPR LHGLLQPLPI AEGRWLDISM 1210 1220 1230 1240 1250 1260 DFVTGLPPTS NNLNMILVVV DRFSKRAHFI ATRKTLDATQ LIDLLFRYIF SYHGFPRTIT 1270 1280 1290 1300 1310 1320 SDRDVRMTAD KYQELTKRLG IKSTMSSANH PQTDGQSERT IQTLNRLLRA YVSTNIQNWH 1330 1340 1350 1360 1370 1380 VYLPQIEFVY NSTPTRTLGK SPFEIDLGYL PNTPAIKSDD EVNARSFTAV ELAKHLKALT 1390 1400 1410 1420 1430 1440 IQTKEQLEHA QIEMETNNNQ RRKPLLLNIG DHVLVHRDAY FKKGAYMKVQ QIYVGPFRVV 1450 1460 1470 1480 1490 KKINDNAYEL DLNSHKKKHR VINVQFLKSL YTVQTRTQRI NQSAPLRELR EHTKLLHS
	Isoform Transposon Ty3-I Gag polyprotein [UniParc]. See Q99219.		–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses." Hansen L.J., Chalker D.L., Sandmeyer S.B. Mol. Cell. Biol. 8:5245-5256(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX." Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:84-87(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein." Hansen L.J., Sandmeyer S.B. J. Virol. 64:2599-2607(1990) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[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	M23367 Genomic DNA. Translation: AAA35184.1. Sequence problems. Z46728 Genomic DNA. Translation: CAA86713.1. Sequence problems. Z37997 Genomic DNA. Translation: CAA86090.1. BK006942 Genomic DNA. Translation: DAA08470.1. Sequence problems.
PIR	S53577.
RefSeq	NP_012184.1. NM_001181434.2.
3D structure databases
ProteinModelPortal	Q7LHG5.
SMR	Q7LHG5. Positions 608-957, 1137-1359.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q7LHG5. 1 interaction.
MINT	MINT-541560.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	854728.
KEGG	sce:YIL082W-A.
Organism-specific databases
SGD	S000003537. YIL082W-A.
Phylogenomic databases
HOGENOM	HOG000172599.
KO	K07497.
OrthoDB	EOG44N213.
Gene expression databases
Genevestigator	Q7LHG5.
Family and domain databases
InterPro	IPR001584. Integrase_cat-core. IPR024650. Peptidase_A2B. IPR021109. Peptidase_aspartic. IPR005162. Retrotrans_gag. IPR012337. RNaseH-like_dom. IPR000477. RVT. IPR001878. Znf_CCHC. [Graphical view]
Pfam	PF12384. Peptidase_A2B. 1 hit. PF03732. Retrotrans_gag. 1 hit. PF00665. rve. 1 hit. PF00078. RVT_1. 1 hit. [Graphical view]
SMART	SM00343. ZnF_C2HC. 1 hit. [Graphical view]
SUPFAM	SSF50630. Pept_Aspartic. 1 hit. SSF53098. RNaseH_fold. 1 hit.
PROSITE	PS50994. INTEGRASE. 1 hit. PS50878. RT_POL. 1 hit. PS50158. ZF_CCHC. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	977418.

Entry information

Entry name

YI31B_YEAST

Accession

Primary (citable) accession number: Q7LHG5
Secondary accession number(s): D6VVK4 , Q04717, Q04722, Q05350

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	March 6, 2007
Last modified:	May 1, 2013
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program