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- PDB-6hb5: Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyro... -

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Basic information

Entry
Database: PDB / ID: 6hb5
TitleCrystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-cytidine
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / Rossmann fold / tRNA aminoacylation
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / 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 / 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. / Rossmann-like alpha/beta/alpha sandwich fold ...: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / 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. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
Chem-YSC / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.88 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders1S53518N Belgium
Research Foundation - FlandersG0A4616N Belgium
Research Foundation - FlandersG077814N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.
Authors: Nautiyal, M. / De Graef, S. / Pang, L. / Gadakh, B. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Category: pdbx_database_proc
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,3828
Polymers95,1902
Non-polymers1,1936
Water10,953608
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-25 kcal/mol
Surface area35740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.611, 65.049, 90.686
Angle α, β, γ (deg.)90.000, 101.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 47594.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Gene: tyrS, ECBD_2006 / Plasmid: PETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A140NBN7, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-YSC / [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate


Mass: 485.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23N5O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate (1M stock solution adjusted to pH 6), 20% (v/v) EG. For soaking crystals were transferred to drop ...Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate (1M stock solution adjusted to pH 6), 20% (v/v) EG. For soaking crystals were transferred to drop containing mother liquor supplemented with 2 mM inhibitor.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968625 Å / Relative weight: 1
ReflectionResolution: 1.71→88.91 Å / Num. obs: 98934 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.044 / Rrim(I) all: 0.087 / Net I/σ(I): 8.3 / Num. measured all: 371877
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.71-1.83.81.177142480.6810.6891.36897.6
5.41-88.913.60.0433070.9980.0230.04699.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.88→27.53 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2103 2.81 %RANDOM
Rwork0.193 ---
obs0.194 74837 98.5 %-
Displacement parametersBiso max: 185.63 Å2 / Biso mean: 41.02 Å2 / Biso min: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.9886 Å20 Å24.5768 Å2
2---10.8726 Å20 Å2
3---0.8839 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.88→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6462 0 79 608 7149
Biso mean--31.03 45.51 -
Num. residues----830
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2326SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes195HARMONIC2
X-RAY DIFFRACTIONt_gen_planes996HARMONIC5
X-RAY DIFFRACTIONt_it6677HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion858SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8400SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6677HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9037HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion16.47
LS refinement shellResolution: 1.88→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2286 140 2.54 %
Rwork0.2162 5369 -
all0.2165 5509 -
obs--97.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33460.05070.27970.7803-0.21130.8266-0.01610.16890.0519-0.02960.01820.0261-0.024-0.0221-0.00210.11880.0019-0.00560.13570.00590.1488-50.02331.8472-45.7999
22.825-0.19570.11770.2119-0.0170.69690.0210.33430.05750.0666-0.04360.0077-0.03390.1390.02250.1515-0.0097-0.00690.20570.03980.1834-85.13915.2374-57.956
30.9767-0.01641.34220.4662-0.04922.1343-0.0217-0.1869-0.02040.08010.02810.0112-0.0731-0.1375-0.00640.19040.01410.00690.224-0.01190.1524-37.49972.2051-9.2407
42.4188-0.955-0.85393.86870.56410.82820.08630.00030.2156-0.3232-0.001-0.9181-0.17340.1301-0.08530.2077-0.04140.0350.34440.02440.3185-7.41987.67784.0711
53.77265.16380.703900.16343.8321-0.1119-0.0983-0.7373-0.05750.1301-0.8440.03420.7377-0.01820.25820.04530.24450.5369-0.01920.982310.7063.1763-1.6137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|252 }A5 - 252
2X-RAY DIFFRACTION2{ A|253 - A|424 }A253 - 424
3X-RAY DIFFRACTION3{ B|5 - B|252 }B5 - 252
4X-RAY DIFFRACTION4{ B|253 - B|386 }B253 - 386
5X-RAY DIFFRACTION5{ B|387 - B|424 }B387 - 424

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