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6.1.1.1: tyrosine-tRNA ligase

This is an abbreviated version!
For detailed information about tyrosine-tRNA ligase, go to the full flat file.

Word Map on EC 6.1.1.1

Reaction

ATP
+
L-tyrosine
 +
tRNATyr
=
AMP
 +
diphosphate
 +
L-tyrosyl-tRNATyr

Synonyms

CHOTyrRS, class I tyrosyl-tRNA synthetase, CYT-18, CYT-18 protein, dTyRS, hTyrRS, LdTyrRS, LMJF_14_1370, mini-tyrosyl-tRNA synthetase, mini-TyrRS, mitochondrial tyrosyl-tRNA synthetase, MjYRS, mt-TyrRS, mtTyrRS, NpAla TyrRS, p-BrPhe TyrRS, tRNATyr/tyrosyl-tRNA synthetase, Tyrosine translase, Tyrosine tRNA synthetase, Tyrosine--tRNA ligase, Tyrosine-transfer ribonucleate synthetase, Tyrosine-transfer RNA ligase, tyrosyl aminoacyl-tRNA synthetase, tyrosyl synthetase, tyrosyl tRNA synthetase, Tyrosyl--tRNA ligase, Tyrosyl-transfer ribonucleate synthetase, Tyrosyl-transfer ribonucleic acid synthetase, Tyrosyl-transfer RNA synthetase, Tyrosyl-tRNA ligase, Tyrosyl-tRNA synthetase, tyrosyl—tRNA synthetase, TyrRS, TyrRSs, TyrRZ, tyrS, TYS1, YARS, YRS, YTS

ECTree

     6 Ligases
         6.1 Forming carbon-oxygen bonds
             6.1.1 Ligases forming aminoacyl-tRNA and related compounds
                6.1.1.1 tyrosine-tRNA ligase

Crystallization

Crystallization on EC 6.1.1.1 - tyrosine-tRNA ligase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified selenomethionyl-TyrRSapm in complex with tyrosinol, crystallization is improved by introducing anion-exchange chromatography, vapour diffusion method, 0.002 ml of 14 mg/ml protein in 20 mM Tris-HCl, pH 7.4, 25°C, is mixed with 500 nl reservoir solution containing 0.1 M sodium citrate, pH 5.5, and 6-9% PEG 4000 w/v, 15% 2-methyl-2,4-pentane-d12-diol, 0.1 M KCl, 1 mM MgCl2, X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement
crystal of SeMet-substituted TyrRS is obtained by the microbatch method, using an automatic crystallization robot. The crystals are grown at 20°C in a month. The crystal of native TyrRS is obtained by hanging-drop, vapor-diffusion method. Crystals of SeMet-substituted TyrRS belong to the space group P4(3)2(1)2, with unit cell parameters a = b = 66.66 A, c = 197.48 A. Crystals of native TyrRS belong to the space group P4(3)2(1)2 with unit cell parameters a = b = 65.91 A, c = 196.17 A
hanging-drop vapour-diffusion method, The crystals belong to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 66.1, c= 196.2 A, and diffract to beyond 2.15 A resolution
hanging-drop, vapor-diffusion method. Crystals belong to the space group P2(1), with unit cell parameters a = 40.62 A, b = 96.16 A, c = 92.64 A, beta = 94.41°
hanging drop vapor-diffusion method. Crystal structures of TyrRS catalytic domain, in complex with L-tyrosine and L-tyrosyladenylate analogue, 5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine, are solved at 2.0 A and 2.7 A resolution
the iodoTyrRS-ec-3-azide-L-tyrosine structure is determined at a resolution of 1.8 A
electron density map, X-ray structure
-
3
quarternary structure
-
4
T51 mutants of tyrosyl-tRNA synthetase
X-ray diffraction, at 2.7 A resolution, structure analysis of the enzyme-ligand complex, e.g. with specific synthetic inhibitors, molecular modeling
-
mutant mt-TyrRS-DS4, lacking the C-terminal S4-like domain, in complex with Tyr-AMS, an adenylate analogue, X-ray diffraction structure determination and analysis at 2.2 A resolution, molecular replacement
-
purified tyrosyl-tRNA synthetase in complex with a nanobody and inhibitory tyrosyl adenylate analogue TyrSA, purified LdTyrRS and NbA proteins are incubated on ice for 30 min at a 1:2 M ratio followed by buffer exchange to crystallization buffer. The protein complex is then incubated with 0.2 mM of TyrSA (5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine) on ice for 30-60 min, sitting drop vapour diffsuion method, mixing of 0.001 ml of protein solution containing 5 mg/ml protein complex in 25 mM HEPES, pH 7.25, 100 mM NaCl, 1 mM TCEPHCl, 5% glycerol, and 0.025% NaN3, with 0.001 ml of reservoir solution containing 0.1 M sodium cacodylate, pH 5.7, and 22% PEG 4000, room temperature, 5-7 days, X-ray diffraction structure determination and analysis at 2.75 A resolution, modeling
-
purified recombinant C-terminally His6-tagged tyrosyl aminoacyl-tRNA synthetase, sitting-drop vapor diffusion technique, 15 mg/ml protein in 20 mM Tris, pH 8.5, 50 mM NaCl, 10 mM 2-mercaptoethanol, crystals are grown either in the presence of 2 mM 4-bromophenylalanine or 3-(2-naphthyl)alanine at 20°C or 4°C, against a mother liquor composed of 16-20% PEG 300, 3-5% PEG 8000, 100 mM Tris, pH 8.8-pH 8.2, and 10% glycerol by mixing of equla volumes, X-ray diffraction structure determination and analysis at 1.9 A resolution
sitting-drop vapor-diffusion method. Space group P2(1)2(1)2(1) with two molecules per asymmetric unit, with unit cell dimensions a = 45.12 A, b = 185.29 A, and c = 95.48 A. Crystal structures for the apo wild-type and O-methyl-L-tyrosine-specific mutant enzyme are determined at 2.66 A and 3.0 A
structure of the TyrRS-tRNA(Tyr)-L-tyrosine complex, solved at a resolution of 1.95 A
hanging-drop vapour diffusion method. The crystals belong to the monoclinic space group P2(1) with unit-cell parameters a = 49.2 A, b = 156.5 A, c = 55.2 A, beta = 94.2
-
1.95 A crystal structure of mutant DELTA424-669 of CYT-18 protein. DELTA424-669 crystals are grown by sitting-drop vapor diffusion. The crystals are in space group C2 with unit cell dimensions: a = 104.88 A, b = 73.21 A, c = 56.79 A, beta = 111.35°
-
a 4.5 A co-crystal structure of the Twort orf 142-I2 group I intron ribozyme bound to splicing-active, carboxy-terminally truncated CYT-18. Structure shows that the group I intron binds across the two subunits of the homodimeric protein with a newly evolved RNA-binding surface distinct from that which binds tRNATyr. This RNA binding surface provides an extended scaffold for the phosphodiester backbone of the conserved catalytic core of the intron RNA, allowing the protein to promote the splicing of a wide variety of group I introns. The group I intron-binding surface includes three small insertions and additional structural adaptations relative to non-splicing bacterial TyrRSs, indicating a multistep adaptation for splicing function
hanging-drop, vapor-diffusion method. Crystals belong to the space group P2(1)2(1)2(1), with unit cell parameters a = 74.35 A, b = 88.26 A, c = 162.92 A
crystal structure at 2.3 A resolution
-
purified recombinant modified enzyme, SceTyrRS comprising residues 1-364, as ternary complex with cognate tRNATyr and Tyr-AMP analog O-(adenosine-5'-O-yl) N-(L-tyrosyl)phosphoramidate, i.e. Tyr-AMPN, hanging-drop vapor diffusion method, mixing of equal volumes of protein solution containing ca. 0.2 mM SceTyrRS, 5 mM Tyr-AMPN, ca. 0.2 mM tRNATyr, 40 mM KCl in 20 mM Tris buffer at pH 7.5, with reservoir solution containing 25% v/v PEG 400 and 100 mM CaCl2 in 100 mM Tris buffer at pH 7.5, X-ray diffraction structure determination and analysis at 2.4 A resolution
crystal structure determination by X-ray diffraction, enzyme complexed with inhibitors at 2.8 A resolution, and truncated enzyme complexed with inhibitors at 2.2 A resolution
-
enzyme complexed to a tyrosyl aryl dipeptide inhibitor, structure analysis
-
pure enzyme, 12 mg/ml, or in complex with tyrosinol, hanging drop vapour diffusion technique, equal volumes of protein and a reservoir solution that contains 1.2 M ammonium sulfate, 10 mM MgCl2, 0.5 mM dithiothreitol, 50 mM MES, pH 5.8, X-ray diffraction structure determination and analysis, enzyme in complex with tyrosinol, ATP and tRNATyr, at 293K, equilibration of 0.004 ml protein-RNA solution against 1 ml reservoir solution, protein-RNA solution: 4-5 mg/ml of enzyme in a molar ratio of 1:1 or 1:2 with RNA, 5 mM tyrosinol, 10 mg MgCl2, 10 mM ATP, 50 mM HEPES, pH 7.0, 0.8 M ammonium sulfate, reservoir solution: 1.5-1.6 M ammonium sulfate, 0.1 M HEPES, pH 7.0, 2-4 weeks, X-ray diffraction structure determination at 2.0-2.1 A resolution and analysis
-