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- PDB-8uk6: Candida albicans glutaminyl tRNA synthetase (GLN4) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8uk6
TitleCandida albicans glutaminyl tRNA synthetase (GLN4) in complex with N-pyrimidinyl-beta-thiophenylacrylamide
Componentsglutamine--tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / Inhibitor / Complex / Allosteric / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / mitochondrion / ATP binding / cytosol
Similarity search - Function
Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Glutamine-tRNA synthetase / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain ...Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Glutamine-tRNA synthetase / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
: / glutamine--tRNA ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsSychantha, D. / Wright, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institute for Advanced Research (CIFAR)CF-0182 Canada
CitationJournal: Cell Chem Biol / Year: 2024
Title: Allosteric inhibition of tRNA synthetase Gln4 by N-pyrimidinyl-beta-thiophenylacrylamides exerts highly selective antifungal activity.
Authors: Puumala, E. / Sychantha, D. / Lach, E. / Reeves, S. / Nabeela, S. / Fogal, M. / Nigam, A. / Johnson, J.W. / Aspuru-Guzik, A. / Shapiro, R.S. / Uppuluri, P. / Kalyaanamoorthy, S. / Magolan, J. ...Authors: Puumala, E. / Sychantha, D. / Lach, E. / Reeves, S. / Nabeela, S. / Fogal, M. / Nigam, A. / Johnson, J.W. / Aspuru-Guzik, A. / Shapiro, R.S. / Uppuluri, P. / Kalyaanamoorthy, S. / Magolan, J. / Whitesell, L. / Robbins, N. / Wright, G.D. / Cowen, L.E.
History
DepositionOct 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutamine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7843
Polymers93,4871
Non-polymers2972
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.090, 143.090, 145.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-933-

HOH

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Components

#1: Protein glutamine--tRNA ligase


Mass: 93487.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: GLN4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1D8PQM9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-WVK / (2E)-N-(pyrimidin-2-yl)-3-(thiophen-2-yl)prop-2-enamide


Mass: 231.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9N3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium thiocyanate, 22% PEG 3350 with micro seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.73→45.99 Å / Num. obs: 20414 / % possible obs: 99.92 % / Redundancy: 26.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.04414 / Rrim(I) all: 0.2274 / Net I/σ(I): 18.65
Reflection shellResolution: 2.73→2.828 Å / Redundancy: 27 % / Rmerge(I) obs: 2.571 / Mean I/σ(I) obs: 2.571 / Num. unique obs: 2006 / CC1/2: 0.787 / CC star: 0.939 / Rpim(I) all: 0.5024 / Rrim(I) all: 2.62 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→45.99 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 1979 9.7 %
Rwork0.2032 --
obs0.2068 20411 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 17 33 4727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034811
X-RAY DIFFRACTIONf_angle_d0.5076502
X-RAY DIFFRACTIONf_dihedral_angle_d13.7511840
X-RAY DIFFRACTIONf_chiral_restr0.043686
X-RAY DIFFRACTIONf_plane_restr0.005860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.80.34261420.31851289X-RAY DIFFRACTION100
2.8-2.870.30271330.29881293X-RAY DIFFRACTION100
2.87-2.960.33081420.27091293X-RAY DIFFRACTION100
2.96-3.050.31161400.27041299X-RAY DIFFRACTION100
3.05-3.160.3191360.26821298X-RAY DIFFRACTION100
3.16-3.290.29821420.26041296X-RAY DIFFRACTION100
3.29-3.440.25551380.22151301X-RAY DIFFRACTION100
3.44-3.620.26311420.21791302X-RAY DIFFRACTION100
3.62-3.850.2141390.21361314X-RAY DIFFRACTION100
3.85-4.140.24091440.20281310X-RAY DIFFRACTION100
4.14-4.560.21491400.1641329X-RAY DIFFRACTION100
4.56-5.220.19841450.16571330X-RAY DIFFRACTION100
5.22-6.570.22631450.19111351X-RAY DIFFRACTION100
6.58-45.990.21461510.16921427X-RAY DIFFRACTION100
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)
13.81511.2606-0.37076.38840.6581.4194-0.03370.1137-0.18610.1641-0.06210.75340.6114-0.54030.05760.8758-0.2918-0.0420.5750.01320.510733.9187.811319.9693
21.44160.7248-0.51598.56671.11741.27030.245-0.3136-0.32750.7815-0.2744-0.82440.81060.09020.05741.1563-0.1508-0.2250.50810.08450.641547.31535.39227.3851
32.1071-0.6404-0.40462.21730.16142.62990.01370.1124-0.47780.48940.1982-0.51250.98850.3204-0.20271.3577-0.0687-0.25280.5282-0.10150.787351.3865-8.585114.9595
41.35270.1904-0.08346.66190.82341.59550.05950.12260.0128-0.46810.0085-0.45020.2879-0.1772-0.04070.4445-0.07480.00890.3990.04420.439848.922834.240316.6923
54.4014-0.0994-1.03766.8355-1.83885.8448-0.06760.24910.3839-0.1660.06480.47770.14-0.4243-0.00230.31410.04360.00320.368-0.03630.614646.072462.766620.017
62.66240.079-0.26075.12190.71492.8032-0.0161-0.0639-0.1320.0356-0.0349-0.35530.2152-0.0528-0.01540.4141-0.0872-0.03520.32070.03230.514750.942540.215921.3199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 214 through 281 )
2X-RAY DIFFRACTION2chain 'A' and (resid 282 through 339 )
3X-RAY DIFFRACTION3chain 'A' and (resid 340 through 486 )
4X-RAY DIFFRACTION4chain 'A' and (resid 487 through 589 )
5X-RAY DIFFRACTION5chain 'A' and (resid 590 through 678 )
6X-RAY DIFFRACTION6chain 'A' and (resid 679 through 793 )

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