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- PDB-6hb7: Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyro... -

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Basic information

Entry
Database: PDB / ID: 6hb7
TitleCrystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-N3-methyluridine
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 / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / 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 / RNA-binding S4 domain ...Tyrosine-tRNA ligase, bacterial-type, type 1 / 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 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile.
Similarity search - Domain/homology
Chem-Y3U / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders1S53518N Belgium
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N 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

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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)96,4128
Polymers95,1902
Non-polymers1,2236
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-23 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.622, 64.613, 89.670
Angle α, β, γ (deg.)90.000, 100.980, 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 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-Y3U / [(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate


Mass: 500.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O10S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / 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: 2.44 Å3/Da / Density % sol: 49.56 %
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) ethylene glycol For soaking crystals were ...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) ethylene glycol 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.86→88.03 Å / Num. obs: 76335 / % possible obs: 98.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.061 / Rrim(I) all: 0.113 / Net I/σ(I): 9 / Num. measured all: 272521 / Scaling rejects: 2043
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.86-1.963.60.777111310.6370.4890.92399.2
5.88-88.033.50.04524530.9980.0270.05396.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.85 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2129 2.99 %RANDOM
Rwork0.2 ---
obs0.201 71119 98.5 %-
Displacement parametersBiso max: 128.78 Å2 / Biso mean: 39.51 Å2 / Biso min: 15.34 Å2
Baniso -1Baniso -2Baniso -3
1-7.1448 Å20 Å28.8352 Å2
2---3.6594 Å20 Å2
3----3.4854 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.9→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6387 0 81 608 7076
Biso mean--30.13 45.41 -
Num. residues----824
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2291SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes190HARMONIC2
X-RAY DIFFRACTIONt_gen_planes995HARMONIC5
X-RAY DIFFRACTIONt_it6616HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion854SEMIHARMONIC5
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_contact8216SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6616HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8966HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion16.27
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3164 163 3.1 %
Rwork0.2641 5094 -
all0.2656 5257 -
obs--98.87 %
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)
11.197-0.24391.89510.8991-0.37952.93680.0544-0.2667-0.09130.0760.03470.0914-0.0186-0.2514-0.08910.2124-0.01360.01860.21510.0030.1823-38.84582.0275-8.8533
21.8735-0.80930.47913.00671.05974.4181-0.20340.10490.10910.22970.1348-0.3508-0.34130.44990.06860.2653-0.0801-0.04870.31160.03090.1838-16.9377.8168.0461
37.55160.7074-0.80630.6709-0.39462.8270.1580.16340.0711-0.17360.1549-0.32710.16970.4402-0.3130.34360.08720.05280.5732-0.23980.63198.67765.0135-4.5921
41.37250.10130.30531.1178-0.2850.88-0.0130.17540.0238-0.01670.0359-0.01760.0038-0.0233-0.02290.13020.00230.02660.12580.01440.1467-48.90941.505-44.9118
54.35231.33650.86943.9788-2.00531.683-0.15590.2350.30640.1533-0.02730.0137-0.2252-0.06760.18330.12940.02080.01660.16310.01580.1673-72.67834.9684-53.8423
62.5369-0.00220.03430.2347-0.16910.5436-0.03330.27230.09180.0409-0.02380.0553-0.04310.09380.05710.1479-0.01580.03590.15840.04120.1486-86.54695.0187-57.3615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|4 - B|243 }B4 - 243
2X-RAY DIFFRACTION2{ B|244 - B|329 }B244 - 329
3X-RAY DIFFRACTION3{ B|330 - B|424 }B330 - 424
4X-RAY DIFFRACTION4{ A|5 - A|235 }A5 - 235
5X-RAY DIFFRACTION5{ A|236 - A|264 }A236 - 264
6X-RAY DIFFRACTION6{ A|265 - A|424 }A265 - 424

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