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Tyrosine--tRNA ligase, cytoplasmic (EC 6.1.1.1) (Tyrosyl-tRNA synthetase) (TyrRS)

 SYYC_YEAST              Reviewed;         394 AA.
P36421; D6VUW8;
01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
23-MAY-2018, entry version 165.
RecName: Full=Tyrosine--tRNA ligase, cytoplasmic;
EC=6.1.1.1;
AltName: Full=Tyrosyl-tRNA synthetase;
Short=TyrRS;
Name=TYS1; Synonyms=MGM104; OrderedLocusNames=YGR185C; ORFNames=G7522;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=8509419;
Chow C.M., RajBhandary U.L.;
"Saccharomyces cerevisiae cytoplasmic tyrosyl-tRNA synthetase gene.
Isolation by complementation of a mutant Escherichia coli suppressor
tRNA defective in aminoacylation and sequence analysis.";
J. Biol. Chem. 268:12855-12863(1993).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=9294037; DOI=10.1007/s004380050525;
Guan M.-X.;
"Cytoplasmic tyrosyl-tRNA synthetase rescues the defect in
mitochondrial genome maintenance caused by the nuclear mutation
mgm104-1 in the yeast Saccharomyces cerevisiae.";
Mol. Gen. Genet. 255:525-532(1997).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9133739;
DOI=10.1002/(SICI)1097-0061(19970330)13:4<357::AID-YEA77>3.0.CO;2-J;
Arroyo J., Garcia-Gonzalez M., Garcia-Saez M.I., Sanchez-Perez M.,
Nombela C.;
"DNA sequence analysis of a 23,002 bp DNA fragment of the right arm of
Saccharomyces cerevisiae chromosome VII.";
Yeast 13:357-363(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
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.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[5]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-36.
STRAIN=ATCC 208279 / BJ926;
PubMed=7995524; DOI=10.1101/gad.8.23.2868;
Henry N.L., Campbell A.M., Feaver W.J., Poon D., Weil P.A.,
Kornberg R.D.;
"TFIIF-TAF-RNA polymerase II connection.";
Genes Dev. 8:2868-2878(1994).
[7]
PROTEIN SEQUENCE OF 2-18 AND 324-338, CLEAVAGE OF INITIATOR
METHIONINE, ACETYLATION AT SER-2, AND IDENTIFICATION BY MASS
SPECTROMETRY.
Bienvenut W.V., Peters C.;
Submitted (JUN-2005) to UniProtKB.
[8]
SUBUNIT, AND ENZYME REGULATION.
PubMed=328277; DOI=10.1111/j.1432-1033.1977.tb11556.x;
Faulhammer H.G., Cramer F.;
"Tyroslyl-tRNA synthetase from baker's yeast. Rapid isolation by
affinity elution, molecular weight of the enzyme, and determination of
essential sulfhydryl groups.";
Eur. J. Biochem. 75:561-570(1977).
[9]
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=3535890; DOI=10.1021/bi00367a072;
Bare L.A., Uhlenbeck O.C.;
"Specific substitution into the anticodon loop of yeast tyrosine
transfer RNA.";
Biochemistry 25:5825-5830(1986).
[10]
FUNCTION.
PubMed=10588711; DOI=10.1073/pnas.96.25.14366;
Sarkar S., Azad A.K., Hopper A.K.;
"Nuclear tRNA aminoacylation and its role in nuclear export of
endogenous tRNAs in Saccharomyces cerevisiae.";
Proc. Natl. Acad. Sci. U.S.A. 96:14366-14371(1999).
[11]
FUNCTION.
PubMed=10677221; DOI=10.1021/bi992276t;
Fechter P., Rudinger-Thirion J., Theobald-Dietrich A., Giege R.;
"Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is
more sensitive to identity nucleotides than to structural features.";
Biochemistry 39:1725-1733(2000).
[12]
FUNCTION.
STRAIN=YP-ALS;
PubMed=10766779; DOI=10.1074/jbc.275.16.11626;
Soutourina J., Blanquet S., Plateau P.;
"D-tyrosyl-tRNA(Tyr) metabolism in Saccharomyces cerevisiae.";
J. Biol. Chem. 275:11626-11630(2000).
[13]
INTERACTION WITH KNR4/SMI1.
PubMed=11410349; DOI=10.1111/j.1574-6968.2001.tb10692.x;
Dagkessamanskaia A., Martin-Yken H., Basmaji F., Briza P.,
Francois J.;
"Interaction of Knr4 protein, a protein involved in cell wall
synthesis, with tyrosine tRNA synthetase encoded by TYS1 in
Saccharomyces cerevisiae.";
FEMS Microbiol. Lett. 200:53-58(2001).
[14]
MUTAGENESIS OF TYR-43.
PubMed=11530018; DOI=10.1093/oxfordjournals.jbchem.a003001;
Ohno S., Yokogawa T., Nishikawa K.;
"Changing the amino acid specificity of yeast tyrosyl-tRNA synthetase
by genetic engineering.";
J. Biochem. 130:417-423(2001).
[15]
MUTAGENESIS OF 364-LYS--LYS-368, AND SUBCELLULAR LOCATION.
PubMed=11359929; DOI=10.1091/mbc.12.5.1381;
Azad A.K., Stanford D.R., Sarkar S., Hopper A.K.;
"Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear
export.";
Mol. Biol. Cell 12:1381-1392(2001).
[16]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[17]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[18]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-235 AND THR-359, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[19]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- FUNCTION: Catalyzes the attachment of L-tyrosine to tRNA(Tyr) in a
two-step reaction: L-tyrosine is first activated by ATP to form
Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). The
specificity determinants on tRNA(Tyr) are the base pair C1-G72,
the discriminator residue A73, and the three anticodon bases G34,
U35 and A36. Also involved in nuclear tRNA export. Also attaches
D-Tyr to tRNA(Tyr), this reaction is about 150-fold less efficient
than attachment of L-Tyr (PubMed:10766779).
{ECO:0000269|PubMed:10588711, ECO:0000269|PubMed:10677221,
ECO:0000269|PubMed:10766779}.
-!- CATALYTIC ACTIVITY: ATP + L-tyrosine + tRNA(Tyr) = AMP +
diphosphate + L-tyrosyl-tRNA(Tyr).
-!- ENZYME REGULATION: Inhibited by N-ethylmaleimide and p-
chloromercuribenzoate. {ECO:0000269|PubMed:328277}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=54 nM for tRNA(Tyr) {ECO:0000269|PubMed:3535890};
Vmax=280 nmol/min/mg enzyme for tRNA(Tyr)
{ECO:0000269|PubMed:3535890};
Note=The catalytic activity is reduced by substitutions of
residues forming the specificity determinant on the target
tRNA(Tyr).;
-!- SUBUNIT: Homodimer. Interacts with KNR4/SMI1.
{ECO:0000269|PubMed:11410349, ECO:0000269|PubMed:328277}.
-!- INTERACTION:
P32566:SMI1; NbExp=3; IntAct=EBI-18843, EBI-17452;
-!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Predominantly
cytoplasmic, only a small fraction (about 1.5%) found in the
nucleus.
-!- MISCELLANEOUS: Present with 2710 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase
family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L12221; AAB59329.1; -; mRNA.
EMBL; X71998; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; X99074; CAA67529.1; -; Genomic_DNA.
EMBL; Z72970; CAA97211.1; -; Genomic_DNA.
EMBL; U13015; AAA61641.1; -; Genomic_DNA.
EMBL; BK006941; DAA08279.1; -; Genomic_DNA.
PIR; A45999; A45999.
RefSeq; NP_011701.3; NM_001181314.3.
PDB; 2DLC; X-ray; 2.40 A; X=1-394.
PDBsum; 2DLC; -.
ProteinModelPortal; P36421; -.
SMR; P36421; -.
BioGrid; 33437; 218.
DIP; DIP-5548N; -.
IntAct; P36421; 17.
MINT; P36421; -.
STRING; 4932.YGR185C; -.
iPTMnet; P36421; -.
MaxQB; P36421; -.
PaxDb; P36421; -.
PRIDE; P36421; -.
EnsemblFungi; YGR185C; YGR185C; YGR185C.
GeneID; 853097; -.
KEGG; sce:YGR185C; -.
EuPathDB; FungiDB:YGR185C; -.
SGD; S000003417; TYS1.
GeneTree; ENSGT00790000123100; -.
HOGENOM; HOG000228237; -.
InParanoid; P36421; -.
KO; K01866; -.
OMA; YIGFEIS; -.
OrthoDB; EOG092C2KRE; -.
BioCyc; YEAST:G3O-30875-MONOMER; -.
BRENDA; 6.1.1.1; 984.
EvolutionaryTrace; P36421; -.
PRO; PR:P36421; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0010494; C:cytoplasmic stress granule; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004831; F:tyrosine-tRNA ligase activity; IDA:SGD.
GO; GO:0006437; P:tyrosyl-tRNA aminoacylation; IDA:SGD.
CDD; cd00805; TyrRS_core; 1.
Gene3D; 3.40.50.620; -; 1.
InterPro; IPR002305; aa-tRNA-synth_Ic.
InterPro; IPR014729; Rossmann-like_a/b/a_fold.
InterPro; IPR002307; Tyr-tRNA-ligase.
InterPro; IPR023617; Tyr-tRNA-ligase_arc/euk-type.
Pfam; PF00579; tRNA-synt_1b; 1.
PIRSF; PIRSF006588; TyrRS_arch_euk; 1.
PRINTS; PR01040; TRNASYNTHTYR.
TIGRFAMs; TIGR00234; tyrS; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Aminoacyl-tRNA synthetase; ATP-binding;
Complete proteome; Cytoplasm; Direct protein sequencing; Ligase;
Nucleotide-binding; Nucleus; Phosphoprotein; Protein biosynthesis;
Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|Ref.7}.
CHAIN 2 394 Tyrosine--tRNA ligase, cytoplasmic.
/FTId=PRO_0000055676.
MOTIF 48 56 "HIGH" region.
MOTIF 227 231 "KMSKS" region.
MOTIF 360 378 Nuclear localization signal.
BINDING 43 43 Tyrosine. {ECO:0000250}.
BINDING 170 170 Tyrosine. {ECO:0000250}.
BINDING 174 174 Tyrosine. {ECO:0000250}.
BINDING 177 177 Tyrosine. {ECO:0000250}.
BINDING 192 192 Tyrosine. {ECO:0000250}.
MOD_RES 2 2 N-acetylserine. {ECO:0000269|Ref.7}.
MOD_RES 235 235 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 359 359 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
MUTAGEN 43 43 Y->G: Decreases catalytic activity for L-
tyrosine 400-fold, but allows the
utilization of 3-iodo-L-tyrosine and
other 3-modified tyrosines as substrates.
{ECO:0000269|PubMed:11530018}.
MUTAGEN 364 368 KKAKK->EEAEE: Abolishes nuclear
localization.
{ECO:0000269|PubMed:11359929}.
HELIX 9 17 {ECO:0000244|PDB:2DLC}.
STRAND 21 24 {ECO:0000244|PDB:2DLC}.
HELIX 26 34 {ECO:0000244|PDB:2DLC}.
STRAND 41 46 {ECO:0000244|PDB:2DLC}.
HELIX 54 56 {ECO:0000244|PDB:2DLC}.
HELIX 57 68 {ECO:0000244|PDB:2DLC}.
STRAND 72 77 {ECO:0000244|PDB:2DLC}.
HELIX 79 84 {ECO:0000244|PDB:2DLC}.
TURN 85 87 {ECO:0000244|PDB:2DLC}.
HELIX 93 111 {ECO:0000244|PDB:2DLC}.
STRAND 120 123 {ECO:0000244|PDB:2DLC}.
HELIX 125 128 {ECO:0000244|PDB:2DLC}.
HELIX 131 141 {ECO:0000244|PDB:2DLC}.
HELIX 146 152 {ECO:0000244|PDB:2DLC}.
TURN 153 156 {ECO:0000244|PDB:2DLC}.
HELIX 166 180 {ECO:0000244|PDB:2DLC}.
STRAND 184 189 {ECO:0000244|PDB:2DLC}.
HELIX 190 192 {ECO:0000244|PDB:2DLC}.
HELIX 193 202 {ECO:0000244|PDB:2DLC}.
HELIX 203 206 {ECO:0000244|PDB:2DLC}.
STRAND 212 216 {ECO:0000244|PDB:2DLC}.
HELIX 243 252 {ECO:0000244|PDB:2DLC}.
HELIX 264 271 {ECO:0000244|PDB:2DLC}.
HELIX 273 278 {ECO:0000244|PDB:2DLC}.
STRAND 280 282 {ECO:0000244|PDB:2DLC}.
STRAND 288 290 {ECO:0000244|PDB:2DLC}.
HELIX 294 296 {ECO:0000244|PDB:2DLC}.
STRAND 300 304 {ECO:0000244|PDB:2DLC}.
HELIX 305 313 {ECO:0000244|PDB:2DLC}.
HELIX 319 343 {ECO:0000244|PDB:2DLC}.
HELIX 345 354 {ECO:0000244|PDB:2DLC}.
SEQUENCE 394 AA; 44020 MW; 57E8DB9BE6D054B7 CRC64;
MSSAATVDPN EAFGLITKNL QEVLNPQIIK DVLEVQKRHL KLYWGTAPTG RPHCGYFVPM
TKLADFLKAG CEVTVLLADL HAFLDNMKAP LEVVNYRAKY YELTIKAILR SINVPIEKLK
FVVGSSYQLT PDYTMDIFRL SNIVSQNDAK RAGADVVKQV ANPLLSGLIY PLMQALDEQF
LDVDCQFGGV DQRKIFVLAE ENLPSLGYKK RAHLMNPMVP GLAQGGKMSA SDPNSKIDLL
EEPKQVKKKI NSAFCSPGNV EENGLLSFVQ YVIAPIQELK FGTNHFEFFI DRPEKFGGPI
TYKSFEEMKL AFKEEKLSPP DLKIGVADAI NELLEPIRQE FANNKEFQEA SEKGYPVATP
QKSKKAKKPK NKGTKYPGAT KTNEIATKLE ETKL


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