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- PDB-6i5y: Crystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyro... -

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Basic information

Entry
Database: PDB / ID: 6i5y
TitleCrystal structure of E. coli tyrRS in complex with 5'-O-(N-L-tyrosyl)sulfamoyl-adenosine
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
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionNov 15, 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 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)96,3957
Polymers95,1902
Non-polymers1,2055
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-12 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.393, 66.508, 91.710
Angle α, β, γ (deg.)90.000, 101.730, 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-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O8S / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
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 pH 6 (1M stock solution adjusted to pH 5) and 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 pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were transferred to a drop containing mother liquor supplemented with 2 mM inhibitor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979292 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2018
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979292 Å / Relative weight: 1
ReflectionResolution: 1.8→79.7 Å / Num. obs: 87607 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.93.60.878126200.7460.5341.02997.7
5.69-79.73.50.04929220.9950.030.05899.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUD

4oud


Resolution: 1.9→79.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2239 3 %RANDOM
Rwork0.193 ---
obs0.194 74654 98.5 %-
Displacement parametersBiso max: 140.93 Å2 / Biso mean: 42.52 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.8606 Å20 Å20.1504 Å2
2---9.455 Å20 Å2
3---2.5944 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.9→79.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 0 82 734 7230
Biso mean--34.16 51.89 -
Num. residues----826
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2282SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes188HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1005HARMONIC5
X-RAY DIFFRACTIONt_it6631HARMONIC20
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_contact8267SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6631HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8986HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion15.86
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2352 167 3.05 %
Rwork0.2077 5306 -
all0.2085 5473 -
obs--97.62 %
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)
10.9075-0.01510.65590.62340.05552.3719-0.03270.0397-0.03380.0162-0.0061-0.0061-0.0699-0.03980.03870.22980.00230.00340.1324-0.01610.2072-38.68161.7356-9.3766
22.9427-0.8211-0.04631.28590.34362.298-0.1196-0.19590.19310.06040.0224-0.1699-0.19110.29360.09720.214-0.0172-0.03870.2152-0.00140.2103-17.28617.63068.0907
37.39410.4921-1.74710.37990.26211.74250.0672-0.2090.2080.04250.1533-0.0053-0.14320.1547-0.22050.27180.03250.03930.3668-0.03480.36539.40954.5751-2.7002
41.3706-0.09630.7730.8553-0.32712.22050.00030.22910.0154-0.04790.02850.03970.0216-0.0322-0.02880.2026-0.010.00880.3041-0.01140.1986-48.6650.5854-45.0727
52.23850.2276-0.23991.111-0.22660.9077-0.02280.31680.2634-0.0053-0.1049-0.0044-0.23510.06530.12780.24660.0041-0.01040.35850.01590.2421-44.22236.7268-48.4737
62.56040.92790.13161.5609-0.58090.9635-0.061-0.15810.22720.051-0.01860.0396-0.194-0.35090.07960.22920.0269-0.02760.54080.03110.2868-71.49185.4683-55.0021
73.08910.053-0.28920.2612-0.2595-0.25330.0835-0.2242-0.08810.0882-0.05350.0524-0.08780.1206-0.030.2517-0.02240.00590.54860.03930.2179-85.27315.4588-58.2168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|5 - B|235 }B5 - 235
2X-RAY DIFFRACTION2{ B|236 - B|329 }B236 - 329
3X-RAY DIFFRACTION3{ B|330 - B|424 }B330 - 424
4X-RAY DIFFRACTION4{ A|5 - A|191 }A5 - 191
5X-RAY DIFFRACTION5{ A|192 - A|235 }A192 - 235
6X-RAY DIFFRACTION6{ A|236 - A|264 }A236 - 264
7X-RAY DIFFRACTION7{ A|265 - A|424 }A265 - 424

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