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- PDB-4ts1: CRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHET... -

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Basic information

Entry
Database: PDB / ID: 4ts1
TitleCRYSTAL STRUCTURE OF A DELETION MUTANT OF A TYROSYL-T/RNA SYNTHETASE COMPLEXED WITH TYROSINE
ComponentsTYROSYL-tRNA SYNTHETASE
KeywordsLIGASE (SYNTHETASE)
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
AuthorsBrick, P. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine.
Authors: Brick, P. / Blow, D.M.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of Tyrosyl-T/RNA Synthetase Refined at 2.3 Angstroms Resolution. Interaction of the Enzyme with the Tyrosyl Adenylate Intermediate
Authors: Brick, P. / Bhat, T.N. / Blow, D.M.
#2: 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.
#3: Journal: Embo J. / Year: 1983
Title: Deletion Mutagenesis Using an M13 Splint. The N-Terminal Structural Domain of Tyrosyl-T/RNA Synthetase (B. Stearothermophilus) Catalyses the Formation of Tyrosyl Adenylate
Authors: Waye, M.M.Y. / Winter, G. / Wilkinson, A.J. / Fersht, A.R.
#4: 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.
#5: 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.
History
DepositionJun 29, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_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_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
A: TYROSYL-tRNA SYNTHETASE
B: TYROSYL-tRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0774
Polymers72,7142
Non-polymers3622
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-28 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.460, 67.060, 61.370
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: MET 1 - SIDE CHAIN OMITTED IN CHAINS A AND B. / 2: LYS 83 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B. / 3: SER 84 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN B. / 4: ARG 86 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B. / 5: THR 87 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN A. / 6: LYS 91 - SIDE CHAIN BEYOND CG OMITTED IN CHAINS A AND B. / 7: GLU 92 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B. / 8: ARG 100 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A.
9: GLU 103 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
10: GLU 112 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
11: ASP 114 - SIDE CHAIN OMITTED IN CHAINS A.
12: GLN 155 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
13: ILE 158 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN A. - SIDE CHAIN BEYOND CG OMITTED IN CHAIN B.
14: GLU 159 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
15: ARG 214 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
16: ILE 222 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
17: LYS 230 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A. - SIDE CHAIN BEYOND CB OMITTED IN CHAIN B.
18: LYS 233 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
19: THR 234 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
20: GLU 235 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
21: SER 236 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN A. / 22: LYS 243 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN B.
23: GLU 276 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A. - SIDE CHAIN BEYOND CB OMITTED IN CHAIN B.
24: GLN 283 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN A.
25: ARG 286 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
26: GLU 287 - SIDE CHAIN BEYOND CG OMITTED IN CHAINS A AND B.
27: GLU 290 - SIDE CHAIN BEYOND CB OMITTED IN CHAINS A AND B.
28: LYS 291 - SIDE CHAIN BEYOND CG OMITTED IN CHAINS A AND B.
29: ARG 292 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A. / 30: LYS 296 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A. / 31: GLU 309 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN B.
32: GLU 310 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A. - SIDE CHAIN BEYOND CB OMITTED IN CHAIN B.
33: ARG 313 - SIDE CHAIN BEYOND CB OMITTED IN A AND B. / 34: GLU 314 - SIDE CHAIN BEYOND CG OMITTED IN CHAIN A. / 35: ARG 317 - SIDE CHAIN BEYOND CB OMITTED IN CHAIN A.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1606, -0.7198, 0.6754), (-0.7351, -0.3694, -0.5685), (0.6587, -0.5877, -0.4698)22.91, 33.08, 7.05
2given(-0.0936, -0.7155, 0.6923), (-0.7722, -0.3868, -0.5042), (0.6285, -0.5817, -0.5163)19.78, 35.47, 7.73
DetailsTHE TRANSFORMATION PROVIDED ON THE *MTRIX 1* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR RESIDUES 1-220 OF THE *A* CHAIN WHEN APPLIED TO THE EQUIVALENT RESIDUES OF THE *B* CHAIN. THE TRANSFORMATION PROVIDED ON THE *MTRIX 2* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR RESIDUES 221-313 OF THE *A* CHAIN WHEN APPLIED TO THE EQUIVALENT RESIDUES OF THE *B* CHAIN.

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Components

#1: Protein TYROSYL-tRNA SYNTHETASE


Mass: 36357.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: M13 / References: UniProt: P00952, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mMprotein1drop
21 mMtyrosine1drop
36 %(w/v)polyethylene glycol 40001drop
412 %polyethylene glycol1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 26176 / % possible obs: 94.3 % / Num. measured all: 64683 / Rmerge(I) obs: 0.058

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å /
RfactorNum. reflection
obs0.187 25459
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 26 144 4990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0440.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.21.5
X-RAY DIFFRACTIONp_mcangle_it4.82.25
X-RAY DIFFRACTIONp_scbond_it3.871.5
X-RAY DIFFRACTIONp_scangle_it5.792.25
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.30.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å / Highest resolution: 2.5 Å / Num. reflection obs: 25459 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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