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- PDB-1y5w: tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-... -

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Basic information

Entry
Database: PDB / ID: 1y5w
TitletRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
Similarity search - Function
Queuine tRNA-ribosyltransferase-like / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NEZ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsStengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding
Authors: Stengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G.
#1: Journal: To be Published
Title: Synthesis, Biological Evaluation and Crystallographic Studies of Extended Guanine-based (lin-Benzoguanine) Inhibitors for tRNA-Guanine Transglycosylase (TGT)
Authors: Meyer, E.A. / Donati, N. / Guillot, M. / Schweizer, B. / Diederich, F. / Stengl, B. / Heine, A. / Brenk, R. / Klebe, G.
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 19, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _struct_conn.ptnr1_auth_comp_id ..._pdbx_struct_assembly_prop.biol_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: 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

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3635
Polymers42,7951
Non-polymers5694
Water5,999333
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,72710
Polymers85,5892
Non-polymers1,1388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5700 Å2
ΔGint-24 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.92, 65.25, 69.97
Angle α, β, γ (deg.)90.00, 95.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1239-

HOH

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Components

#1: Protein Queuine tRNA-ribosyltransferase / / tRNA-guanine transglycosylase / Guanine insertion enzyme


Mass: 42794.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NEZ / 6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE


Mass: 319.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N5O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG8000, MES, DMSO, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 19, 2003
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. all: 53930 / Num. obs: 53930 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.042 / Net I/σ(I): 21.4
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1939 / Rsym value: 0.221 / % possible all: 69.3

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.58→10 Å / Num. parameters: 12830 / Num. restraintsaints: 11913 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 2681 5.1 %RANDOM
Rwork0.1573 ---
all0.1585 52915 --
obs0.1573 52915 95.2 %-
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 2714 / Occupancy sum non hydrogen: 3136.5
Refinement stepCycle: LAST / Resolution: 1.58→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 37 333 3137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0

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