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- PDB-1tyd: STRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 1tyd
TitleSTRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE
ComponentsTYROSYL-tRNA SYNTHETASE
KeywordsAMINOACYL-TRNA SYNTHASE
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / regulation of protein complex stability / tRNA binding / protein homodimerization activity / protein-containing complex / ATP binding / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrown, K.A. / De Meester, P. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate.
Authors: Brick, P. / Bhat, T.N. / Blow, D.M.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal Structure of a Deletion Mutant of a Tyrosyl-T/RNA Synthetase Complexed with Tyrosine
Authors: Brick, P. / Blow, D.M.
#2: Journal: Nature / Year: 1987
Title: Structure of a Mutant of Tyrosyl-tRNA Synthetase with Enhanced Catalytic Properties
Authors: Brown, K.A. / Brick, P. / Blow, D.M.
#3: Journal: Biochemistry / Year: 1986
Title: Internal Thermodynamics of Position 51 Mutants and Natural Variants of Tyrosyl-tRNA Synthetase
Authors: Ho, C.K. / Fersht, A.R.
#4: Journal: Biochemistry / Year: 1986
Title: Natural Variation of Tyrosyl-tRNA Synthetase and Comparison with Engineered Mutants
Authors: Jones, M.D. / Lowe, D.M. / Borgford, T. / Fersht, A.R.
#5: Journal: Biochemistry / Year: 1986
Title: Use of Binding Energy in Catalysis Analyzed by Mutagenesis of the Tyrosyl-tRNA Synthetase
Authors: Wells, T.N.C. / Fersht, A.R.
#6: Journal: Biochemistry / Year: 1985
Title: Fine Structure-Activity Analysis of Mutations at Position 51 of Tyrosyl-tRNA Synthetase
Authors: Fersht, A.R. / Wilkinson, A.J. / Carter, P. / Winter, G.
#7: Journal: Cell(Cambridge,Mass.) / Year: 1984
Title: The Use of Double Mutants to Detect Structural Changes in the Active Site of the Tyrosyl-tRNA Synthetase (Bacillus Stearothermophilus)
Authors: Carter, P.J. / Winter, G. / Wilkinson, A.J. / Fersht, A.R.
#8: Journal: Nature / Year: 1984
Title: A Large Increase in Enzyme-Substrate Affinity by Protein Engineering
Authors: Wilkinson, A.J. / Fersht, A.R. / Blow, D.M. / Carter, P. / Winter, G.
#9: Journal: J.Mol.Biol. / Year: 1984
Title: Interaction of Crystalline Tyrosol-T/RNA Synthetase with Adenosine, Adenosine Monophosphate, Adenosine Triphosphate and Pyrophosphate in the Presence of Tyrosinol
Authors: Monteilhet, C. / Blow, D.M. / Brick, P.
#10: Journal: J.Mol.Biol. / Year: 1982
Title: Tyrosyl-T/RNA Synthetase Forms a Mononucleotide-Binding Fold
Authors: Bhat, T.N. / Blow, D.M. / Brick, P. / Nyborg, J.
#11: Journal: Acta Crystallogr.,Sect.A / Year: 1982
Title: A Density-Modification Method for the Improvement of Poorly Resolved Protein Electron-Density Maps
Authors: Bhat, T.N. / Blow, D.M.
#12: Journal: J.Mol.Biol. / Year: 1978
Title: Binding of Tyrosine, Adenosine Triphosphate and Analogues to Crystalline Tyrosyl Transfer RNA Synthetase
Authors: Monteilhet, C. / Blow, D.M.
#13: Journal: Proc.FEBS Meet. / Year: 1978
Title: Structure of Aminoacyl T/RNA Synthetases
Authors: Blow, D.M. / Monteilhet, C. / Rubin, J.R.
#14: Journal: Biochem.Biophys.Res.Commun. / Year: 1977
Title: The Peptide Chain of Tyrosyl T/RNA Synthetase. No Evidence for a Super-Secondary Structure of Four Alpha-Helices
Authors: Blow, D.M. / Irwin, M.J. / Nyborg, J.
#15: Journal: J.Mol.Biol. / Year: 1976
Title: The Crystal Structure of Tyrosyl-Transfer RNA Synthetase at 2.7 Angstroms Resolution
Authors: Irwin, M.J. / Nyborg, J. / Reid, B.R. / Blow, D.M.
#16: Journal: J.Mol.Biol. / Year: 1973
Title: Crystallization and Preliminary X-Ray Diffraction Studies on Tyrosyl-Transfer RNA Synthetase from Bacillus Stearothermophilus
Authors: Reid, B.R. / Koch, G.L.E. / Boulanger, Y. / Hartley, B.S. / Blow, D.M.
History
DepositionJul 6, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TYROSYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4902
Polymers36,3091
Non-polymers1811
Water2,936163
1
E: TYROSYL-tRNA SYNTHETASE
hetero molecules

E: TYROSYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9814
Polymers72,6182
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.460, 64.460, 237.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: MET 1 - SIDE CHAIN OMITTED. / 2: ASP 20 - SIDE CHAIN BEYOND CB OMITTED. / 3: ARG 30 - SIDE CHAIN BEYOND CB OMITTED. / 4: LYS 91 - SIDE CHAIN BEYOND CG OMITTED. / 5: GLU 92 - SIDE CHAIN BEYOND CB OMITTED. / 6: GLU 103 - SIDE CHAIN BEYOND CB OMITTED. / 7: GLU 112 - SIDE CHAIN BEYOND CB OMITTED. / 8: ILE 158 - SIDE CHAIN BEYOND CB OMITTED. / 9: GLU 159 - SIDE CHAIN BEYOND CB OMITTED. / 10: THR 160 - SIDE CHAIN BEYOND CB OMITTED. / 11: ARG 214 - SIDE CHAIN BEYOND CB OMITTED. / 12: LYS 230 - SIDE CHAIN BEYOND CG OMITTED. / 13: LYS 233 - SIDE CHAIN BEYOND CB OMITTED. / 14: GLU 235 - SIDE CHAIN BEYOND CB OMITTED. / 15: SER 236 - SIDE CHAIN BEYOND CB OMITTED. / 16: GLU 276 - SIDE CHAIN BEYOND CG OMITTED. / 17: GLU 284 - SIDE CHAIN BEYOND CB OMITTED. / 18: GLU 287 - SIDE CHAIN BEYOND CG OMITTED. / 19: GLU 290 - SIDE CHAIN BEYOND CB OMITTED. / 20: LYS 291 - SIDE CHAIN BEYOND CG OMITTED. / 21: LYS 296 - SIDE CHAIN BEYOND CG OMITTED. / 22: GLU 310 - SIDE CHAIN BEYOND CB OMITTED. / 23: SER 319 - SIDE CHAIN BEYOND CB OMITTED.

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Components

#1: Protein TYROSYL-tRNA SYNTHETASE


Mass: 36309.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
References: UniProt: P00952, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.65 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Num. obs: 12254 / Rmerge(I) obs: 0.239

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å
Details: THE 83 WATER MOLECULES WITH RESIDUE NUMBERS GREATER THAN 500 PROBABLY REPRESENT DISORDERED PROTEIN.
RfactorNum. reflection
obs0.223 18098
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 13 163 2638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.03
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.751.75
X-RAY DIFFRACTIONp_mcangle_it2.782.25
X-RAY DIFFRACTIONp_scbond_it2.712
X-RAY DIFFRACTIONp_scangle_it42.5
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1120.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor17.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS

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