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

 SYY_METJA               Reviewed;         306 AA.
Q57834;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 1.
25-APR-2018, entry version 132.
RecName: Full=Tyrosine--tRNA ligase;
EC=6.1.1.1;
AltName: Full=Tyrosyl-tRNA synthetase;
Short=TyrRS;
Name=tyrS; OrderedLocusNames=MJ0389;
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 /
JCM 10045 / NBRC 100440) (Methanococcus jannaschii).
Archaea; Euryarchaeota; Methanococci; Methanococcales;
Methanocaldococcaceae; Methanocaldococcus.
NCBI_TaxID=243232;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
PubMed=8688087; DOI=10.1126/science.273.5278.1058;
Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D.,
Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D.,
Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I.,
Overbeek R., Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A.,
Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D.,
Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C.,
Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M.,
Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
"Complete genome sequence of the methanogenic archaeon, Methanococcus
jannaschii.";
Science 273:1058-1073(1996).
[2]
FUNCTION, SUBUNIT, AND KINETIC PARAMETERS.
PubMed=10585437; DOI=10.1074/jbc.274.50.35601;
Steer B.A., Schimmel P.;
"Major anticodon-binding region missing from an archaebacterial tRNA
synthetase.";
J. Biol. Chem. 274:35601-35606(1999).
[3]
MUTAGENESIS OF ASP-286 AND LYS-288.
PubMed=10570126; DOI=10.1073/pnas.96.24.13644;
Steer B.A., Schimmel P.;
"Domain-domain communication in a miniature archaebacterial tRNA
synthetase.";
Proc. Natl. Acad. Sci. U.S.A. 96:13644-13649(1999).
[4]
X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH TRNA(TYR) AND
TYROSINE, MUTAGENESIS OF ASP-286, AND SUBUNIT.
PubMed=12754495; DOI=10.1038/nsb934;
Kobayashi T., Nureki O., Ishitani R., Yaremchuk A., Tukalo M.,
Cusack S., Sakamoto K., Yokoyama S.;
"Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA
synthetases for genetic code expansion.";
Nat. Struct. Biol. 10:425-432(2003).
[5]
X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) OF WILD-TYPE AND
O-METHYL-TYROSINE-SPECIFIC MUTANT APOENZYME.
PubMed=15840835; DOI=10.1110/ps.041239305;
Zhang Y., Wang L., Schultz P.G., Wilson I.A.;
"Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA
synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-
tyrosine.";
Protein Sci. 14:1340-1349(2005).
-!- FUNCTION: Catalyzes the attachment of tyrosine to tRNA(Tyr) in a
two-step reaction: tyrosine is first activated by ATP to form Tyr-
AMP and then transferred to the acceptor end of tRNA(Tyr).
{ECO:0000269|PubMed:10585437}.
-!- CATALYTIC ACTIVITY: ATP + L-tyrosine + tRNA(Tyr) = AMP +
diphosphate + L-tyrosyl-tRNA(Tyr).
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=15 uM for tRNA(Tyr) (at 45 degrees Celsius)
{ECO:0000269|PubMed:10585437};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10585437,
ECO:0000269|PubMed:12754495}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase
family. TyrS type 3 subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L77117; AAB98375.1; -; Genomic_DNA.
PIR; E64348; E64348.
RefSeq; WP_010869888.1; NC_000909.1.
PDB; 1J1U; X-ray; 1.95 A; A=1-306.
PDB; 1U7D; X-ray; 2.65 A; A/B=1-306.
PDB; 1U7X; X-ray; 3.00 A; A/B=1-306.
PDB; 1ZH0; X-ray; 1.90 A; A=1-306.
PDB; 1ZH6; X-ray; 2.50 A; A=1-306.
PDB; 2AG6; X-ray; 1.90 A; A=1-306.
PDB; 2HGZ; X-ray; 2.50 A; A=2-306.
PDB; 2PXH; X-ray; 1.97 A; A=1-306.
PDB; 2ZP1; X-ray; 1.70 A; A=1-306.
PDB; 3D6U; X-ray; 2.20 A; A=1-306.
PDB; 3D6V; X-ray; 2.20 A; A=1-306.
PDB; 3N2Y; X-ray; 2.49 A; A/B=1-306.
PDB; 3QE4; X-ray; 2.30 A; A/B=1-306.
PDB; 4HJR; X-ray; 2.50 A; A/B=1-306.
PDB; 4HJX; X-ray; 2.91 A; A/B=1-306.
PDB; 4HK4; X-ray; 2.30 A; A=1-306.
PDB; 4HPW; X-ray; 2.00 A; A=1-306.
PDB; 4ND6; X-ray; 2.00 A; A=1-306.
PDB; 4ND7; X-ray; 2.00 A; A=1-306.
PDB; 4NDA; X-ray; 1.70 A; A=1-306.
PDB; 4NX2; X-ray; 2.00 A; A=1-306.
PDB; 4PBR; X-ray; 1.90 A; A=1-306.
PDB; 4PBS; X-ray; 2.01 A; A=1-306.
PDB; 4PBT; X-ray; 1.90 A; A=1-306.
PDB; 5L7P; X-ray; 1.90 A; A/B=1-306.
PDB; 5N5U; X-ray; 1.60 A; A=1-306.
PDB; 5N5V; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-306.
PDB; 5U36; X-ray; 3.03 A; A/B=1-306.
PDBsum; 1J1U; -.
PDBsum; 1U7D; -.
PDBsum; 1U7X; -.
PDBsum; 1ZH0; -.
PDBsum; 1ZH6; -.
PDBsum; 2AG6; -.
PDBsum; 2HGZ; -.
PDBsum; 2PXH; -.
PDBsum; 2ZP1; -.
PDBsum; 3D6U; -.
PDBsum; 3D6V; -.
PDBsum; 3N2Y; -.
PDBsum; 3QE4; -.
PDBsum; 4HJR; -.
PDBsum; 4HJX; -.
PDBsum; 4HK4; -.
PDBsum; 4HPW; -.
PDBsum; 4ND6; -.
PDBsum; 4ND7; -.
PDBsum; 4NDA; -.
PDBsum; 4NX2; -.
PDBsum; 4PBR; -.
PDBsum; 4PBS; -.
PDBsum; 4PBT; -.
PDBsum; 5L7P; -.
PDBsum; 5N5U; -.
PDBsum; 5N5V; -.
PDBsum; 5U36; -.
ProteinModelPortal; Q57834; -.
SMR; Q57834; -.
STRING; 243232.MJ_0389; -.
EnsemblBacteria; AAB98375; AAB98375; MJ_0389.
GeneID; 1451246; -.
KEGG; mja:MJ_0389; -.
eggNOG; arCOG01886; Archaea.
eggNOG; COG0162; LUCA.
InParanoid; Q57834; -.
KO; K01866; -.
OMA; YIGFEIS; -.
OrthoDB; POG093Z05HU; -.
PhylomeDB; Q57834; -.
BioCyc; MJAN243232:G1GKE-416-MONOMER; -.
BRENDA; 6.1.1.1; 3260.
EvolutionaryTrace; Q57834; -.
Proteomes; UP000000805; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004831; F:tyrosine-tRNA ligase activity; IBA:GO_Central.
GO; GO:0004832; F:valine-tRNA ligase activity; IBA:GO_Central.
GO; GO:0006437; P:tyrosyl-tRNA aminoacylation; IEA:InterPro.
GO; GO:0006438; P:valyl-tRNA aminoacylation; IBA:GO_Central.
CDD; cd00805; TyrRS_core; 1.
Gene3D; 3.40.50.620; -; 1.
HAMAP; MF_02008; Tyr_tRNA_synth_type3; 1.
InterPro; IPR001412; aa-tRNA-synth_I_CS.
InterPro; IPR002305; aa-tRNA-synth_Ic.
InterPro; IPR014729; Rossmann-like_a/b/a_fold.
InterPro; IPR002307; Tyr-tRNA-ligase.
InterPro; IPR023684; Tyr-tRNA-ligase_3.
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.
PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
1: Evidence at protein level;
3D-structure; Aminoacyl-tRNA synthetase; ATP-binding;
Complete proteome; Cytoplasm; Ligase; Nucleotide-binding;
Protein biosynthesis; Reference proteome.
CHAIN 1 306 Tyrosine--tRNA ligase.
/FTId=PRO_0000055669.
REGION 151 158 Tyrosine.
REGION 228 231 Interaction with t-RNA.
REGION 283 288 Interaction with t-RNA.
MOTIF 37 45 "HIGH" region.
MOTIF 204 208 "KMSKS" region.
BINDING 32 32 Tyrosine. {ECO:0000269|PubMed:12754495}.
BINDING 36 36 Tyrosine. {ECO:0000269|PubMed:12754495}.
BINDING 173 173 Tyrosine. {ECO:0000269|PubMed:12754495}.
BINDING 207 207 ATP. {ECO:0000255}.
SITE 143 143 Interaction with t-RNA.
MUTAGEN 32 32 Y->Q: Confers specificity for the non-
natural amino acid O-methyl-tyrosine;
when associated with T-107; A-158 and P-
162.
MUTAGEN 107 107 E->T: Confers specificity for the non-
natural amino acid O-methyl-tyrosine;
when associated with Q-32; A-158 and P-
162.
MUTAGEN 158 158 D->A: Confers specificity for the non-
natural amino acid O-methyl-tyrosine;
when associated with Q-32; T-107 and P-
162.
MUTAGEN 162 162 L->P: Confers specificity for the non-
natural amino acid O-methyl-tyrosine;
when associated with Q-32; T-107 and A-
158.
MUTAGEN 286 286 D->A: Decreases the rate of
aminoacylation more than 10-fold, without
effect on tyrosyl adenylate synthesis.
{ECO:0000269|PubMed:10570126,
ECO:0000269|PubMed:12754495}.
MUTAGEN 286 286 D->R: Decreases the rate of
aminoacylation with wild-type tRNA and
increases aminoacylation with amber
suppressor tRNA 8-fold. Decreases
affinity for wild-type tRNA and increases
affinity for amber suppressor tRNA.
{ECO:0000269|PubMed:10570126,
ECO:0000269|PubMed:12754495}.
MUTAGEN 288 288 K->A: Decreases the rate of
aminoacylation more than 200-fold,
without effect on tyrosyl adenylate
synthesis. {ECO:0000269|PubMed:10570126}.
HELIX 3 8 {ECO:0000244|PDB:5N5U}.
STRAND 12 15 {ECO:0000244|PDB:5N5U}.
HELIX 17 24 {ECO:0000244|PDB:5N5U}.
STRAND 27 35 {ECO:0000244|PDB:5N5U}.
HELIX 43 57 {ECO:0000244|PDB:5N5U}.
STRAND 60 66 {ECO:0000244|PDB:5N5U}.
HELIX 68 73 {ECO:0000244|PDB:5N5U}.
HELIX 79 95 {ECO:0000244|PDB:5N5U}.
STRAND 101 104 {ECO:0000244|PDB:5N5U}.
HELIX 105 107 {ECO:0000244|PDB:5N5U}.
TURN 108 110 {ECO:0000244|PDB:5N5U}.
HELIX 112 124 {ECO:0000244|PDB:5N5U}.
HELIX 127 133 {ECO:0000244|PDB:5N5U}.
TURN 134 137 {ECO:0000244|PDB:5N5U}.
HELIX 147 162 {ECO:0000244|PDB:5N5U}.
STRAND 165 170 {ECO:0000244|PDB:5N5U}.
HELIX 171 173 {ECO:0000244|PDB:5N5U}.
HELIX 174 183 {ECO:0000244|PDB:5N5U}.
STRAND 184 186 {ECO:0000244|PDB:5N5U}.
STRAND 189 193 {ECO:0000244|PDB:5N5U}.
STRAND 201 204 {ECO:0000244|PDB:5N5U}.
TURN 207 210 {ECO:0000244|PDB:2ZP1}.
STRAND 214 216 {ECO:0000244|PDB:1U7X}.
HELIX 219 227 {ECO:0000244|PDB:5N5U}.
HELIX 240 248 {ECO:0000244|PDB:5N5U}.
STRAND 251 255 {ECO:0000244|PDB:5N5U}.
HELIX 259 261 {ECO:0000244|PDB:5N5U}.
STRAND 265 267 {ECO:0000244|PDB:5N5U}.
HELIX 270 278 {ECO:0000244|PDB:5N5U}.
HELIX 284 306 {ECO:0000244|PDB:5N5U}.
SEQUENCE 306 AA; 35049 MW; 1887760ABAF2DD5E CRC64;
MDEFEMIKRN TSEIISEEEL REVLKKDEKS AYIGFEPSGK IHLGHYLQIK KMIDLQNAGF
DIIILLADLH AYLNQKGELD EIRKIGDYNK KVFEAMGLKA KYVYGSEFQL DKDYTLNVYR
LALKTTLKRA RRSMELIARE DENPKVAEVI YPIMQVNDIH YLGVDVAVGG MEQRKIHMLA
RELLPKKVVC IHNPVLTGLD GEGKMSSSKG NFIAVDDSPE EIRAKIKKAY CPAGVVEGNP
IMEIAKYFLE YPLTIKRPEK FGGDLTVNSY EELESLFKNK ELHPMDLKNA VAEELIKILE
PIRKRL


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