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- PDB-4p3p: Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Sy... -

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Basic information

Entry
Database: PDB / ID: 4p3p
TitleStructural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 3
ComponentsThreonine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / synthetase / inhibitor / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...tRNA aminoacylation / aminoacyl-tRNA ligase activity / threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing 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 / cytosol / cytoplasm
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / 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. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Beta-grasp domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2CR / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsFang, P. / Yu, X. / Chen, K. / Chen, X. / Guo, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106134 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase.
Authors: Fang, P. / Yu, X. / Jeong, S.J. / Mirando, A. / Chen, K. / Chen, X. / Kim, S. / Francklyn, C.S. / Guo, M.
History
DepositionMar 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine--tRNA ligase
B: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,42611
Polymers95,8552
Non-polymers1,5719
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-100 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.534, 107.640, 109.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 47927.516 Da / Num. of mol.: 2 / Fragment: UNP residues 242-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thrS, b1719, JW1709 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2CR / (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid / Borrelidin / Borrelidin


Mass: 489.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H43NO6 / Comment: antibiotic, inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG400, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 66250 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.08 Å2 / Rmerge(I) obs: 0.118 / Χ2: 0.97 / Net I/av σ(I): 15.5 / Net I/σ(I): 4.7 / Num. measured all: 435281
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.186.50.7565830.99699.8
2.18-2.266.50.60365861.03899.7
2.26-2.376.50.49265780.99799.7
2.37-2.496.60.38966040.97699.6
2.49-2.656.40.29665910.98199.5
2.65-2.855.90.21463971.01196.2
2.85-3.1470.15266310.99599.5
3.14-3.5970.0966800.97599.7
3.59-4.526.70.05467450.91899.6
4.52-506.50.0468550.82997.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.1→35.795 Å / FOM work R set: 0.8493 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 3225 5.05 %
Rwork0.1995 60677 -
obs0.2005 63902 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.78 Å2 / Biso mean: 25.62 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 2.1→35.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6497 0 102 626 7225
Biso mean--23.44 34.6 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126782
X-RAY DIFFRACTIONf_angle_d1.229139
X-RAY DIFFRACTIONf_chiral_restr0.093963
X-RAY DIFFRACTIONf_plane_restr0.0051189
X-RAY DIFFRACTIONf_dihedral_angle_d14.6532588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.11790.2107800.26021493157354
2.1179-2.1510.26751110.25982146225778
2.151-2.18630.33611210.25322416253789
2.1863-2.22390.30251420.25582547268993
2.2239-2.26440.29881380.24682637277596
2.2644-2.30790.28891440.24822693283798
2.3079-2.3550.24621600.24692682284299
2.355-2.40620.28031370.24712734287199
2.4062-2.46220.30251580.24522712287099
2.4622-2.52370.25421400.23912735287599
2.5237-2.5920.25171500.23562738288899
2.592-2.66820.26831570.229427162873100
2.6682-2.75430.2351430.22922673281697
2.7543-2.85270.27361480.22072603275195
2.8527-2.96690.22951360.214627692905100
2.9669-3.10180.23821520.206627422894100
3.1018-3.26530.23381370.198327982935100
3.2653-3.46970.20611390.184927662905100
3.4697-3.73730.21211410.173227852926100
3.7373-4.11290.17041530.161228022955100
4.1129-4.70690.14121340.14252806294099
4.7069-5.92590.16661510.16992704285595
5.9259-35.80070.18211530.185829803133100
Refinement TLS params.Method: refined / Origin x: 20.8741 Å / Origin y: 30.3729 Å / Origin z: 20.8211 Å
111213212223313233
T0.0783 Å2-0.0189 Å20.0073 Å2-0.0657 Å20.0017 Å2--0.0603 Å2
L0.4426 °2-0.0423 °2-0.0399 °2-0.5341 °20.0408 °2--0.3618 °2
S0.0047 Å °-0.0142 Å °0.0101 Å °0.0895 Å °-0.0269 Å °0.0247 Å °0.0033 Å °0.0065 Å °0.0112 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA242 - 642
2X-RAY DIFFRACTION1allA650
3X-RAY DIFFRACTION1allD1
4X-RAY DIFFRACTION1allB242 - 642
5X-RAY DIFFRACTION1allB650
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allF1 - 666
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allH1
10X-RAY DIFFRACTION1allI1
11X-RAY DIFFRACTION1allJ1
12X-RAY DIFFRACTION1allK1

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