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- PDB-1kog: Crystal structure of E. coli threonyl-tRNA synthetase interacting... -

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Basic information

Entry
Database: PDB / ID: 1kog
TitleCrystal structure of E. coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator
Components
  • Threonyl-tRNA synthetase
  • Threonyl-tRNA synthetase mRNA
KeywordsLIGASE/RNA / Protein-RNA complex / RNA stem-loop / RNA double helix / RNA base triples / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like / tRNA synthetase class II core domain (G, H, P, S and T) / TGS domain profile. / TGS / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE / RNA / RNA (> 10) / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTorres-Larrios, A. / Dock-Bregeon, A.C. / Romby, P. / Rees, B. / Sankaranarayanan, R. / Caillet, J. / Springer, M. / Ehresmann, C. / Ehresmann, B. / Moras, D.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis of translational control by Escherichia coli threonyl tRNA synthetase.
Authors: Torres-Larios, A. / Dock-Bregeon, A.C. / Romby, P. / Rees, B. / Sankaranarayanan, R. / Caillet, J. / Springer, M. / Ehresmann, C. / Ehresmann, B. / Moras, D.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
I: Threonyl-tRNA synthetase mRNA
J: Threonyl-tRNA synthetase mRNA
K: Threonyl-tRNA synthetase mRNA
L: Threonyl-tRNA synthetase mRNA
M: Threonyl-tRNA synthetase mRNA
N: Threonyl-tRNA synthetase mRNA
O: Threonyl-tRNA synthetase mRNA
P: Threonyl-tRNA synthetase mRNA
A: Threonyl-tRNA synthetase
B: Threonyl-tRNA synthetase
C: Threonyl-tRNA synthetase
D: Threonyl-tRNA synthetase
E: Threonyl-tRNA synthetase
F: Threonyl-tRNA synthetase
G: Threonyl-tRNA synthetase
H: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,57632
Polymers468,47316
Non-polymers4,10316
Water3,063170
1
I: Threonyl-tRNA synthetase mRNA
J: Threonyl-tRNA synthetase mRNA
A: Threonyl-tRNA synthetase
B: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1448
Polymers117,1184
Non-polymers1,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Threonyl-tRNA synthetase mRNA
L: Threonyl-tRNA synthetase mRNA
C: Threonyl-tRNA synthetase
D: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1448
Polymers117,1184
Non-polymers1,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: Threonyl-tRNA synthetase mRNA
N: Threonyl-tRNA synthetase mRNA
E: Threonyl-tRNA synthetase
F: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1448
Polymers117,1184
Non-polymers1,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: Threonyl-tRNA synthetase mRNA
G: Threonyl-tRNA synthetase
hetero molecules

O: Threonyl-tRNA synthetase mRNA
G: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1448
Polymers117,1184
Non-polymers1,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
5
P: Threonyl-tRNA synthetase mRNA
H: Threonyl-tRNA synthetase
hetero molecules

P: Threonyl-tRNA synthetase mRNA
H: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1448
Polymers117,1184
Non-polymers1,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)188.450, 101.740, 199.340
Angle α, β, γ (deg.)90.00, 114.40, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: RNA chain
Threonyl-tRNA synthetase mRNA


Mass: 11833.979 Da / Num. of mol.: 8
Mutation: U(-49)G, U(-48)G, U(-71)C, A(-15)G, A(-14)C, A(-13)C
Source method: obtained synthetically
Details: This is the natural sequence of domain D2 of the trs mRNA operator from E. coli, covering residues -49 to -13 (69 to 105 in the present coordinate file) of E.coli trs mRNA, except for the ...Details: This is the natural sequence of domain D2 of the trs mRNA operator from E. coli, covering residues -49 to -13 (69 to 105 in the present coordinate file) of E.coli trs mRNA, except for the first 3 base pairs. It was synthesized in vitro by T7 transcription.
#2: Protein
Threonyl-tRNA synthetase


Mass: 46725.180 Da / Num. of mol.: 8
Fragment: Catalytic and anticodon binding domains (residues 242 to 642)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-TSB / 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE


Mass: 447.424 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H21N7O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: ammonium sulfate, magnesium chloride, cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2MgCl211
3cacodylate11
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.9 M1
30.088 mMdeltaNThrRS12
40.200 mMd2RNA12
510 mM12MgCl2
610 mMThrAMS12
2sodium cacodylate1pH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.46→30 Å / Num. all: 88408 / Num. obs: 88408 / % possible obs: 97.9 % / Redundancy: 3.74 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.7
Reflection shellResolution: 3.46→3.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4.7 / Num. unique all: 8790 / % possible all: 82.8
Reflection
*PLUS
Lowest resolution: 29.8 Å / Num. measured all: 330893 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 82.8 % / Num. unique obs: 8790 / Num. measured obs: 33319 / Rmerge(I) obs: 0.346

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THREONYL-TRNA SYNTHETASE CORE (PDB CODE: 1EVL)

1evl


Resolution: 3.5→29.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.287 7774 9.9 %RANDOM
Rwork0.251 ---
obs0.251 78341 90 %-
all-87032 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.2087 Å2 / ksol: 0.247445 e/Å3
Displacement parametersBiso mean: 94.6 Å2
Baniso -1Baniso -2Baniso -3
1--16.92 Å20 Å24.34 Å2
2--29.09 Å20 Å2
3----12.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.49 Å
Luzzati d res low-6 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26224 6280 248 170 32922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.073
X-RAY DIFFRACTIONc_mcangle_it5.124
X-RAY DIFFRACTIONc_scbond_it3.834
X-RAY DIFFRACTIONc_scangle_it6.065
LS refinement shellResolution: 3.5→3.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.364 792 9.6 %
Rwork0.327 7475 -
obs--76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3TSA_NEW.PARTSA_NEW.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Num. reflection obs: 78345 / Num. reflection Rfree: 7775 / Rfactor obs: 0.251 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / Num. reflection Rfree: 793 / Rfactor Rwork: 0.328 / Num. reflection Rwork: 7473 / Rfactor obs: 0.328

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