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- PDB-2pot: tRNA guanine transglycosylase (TGT) E235Q mutant in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2pot
TitletRNA guanine transglycosylase (TGT) E235Q mutant in complex with guanine
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / E235Q mutant / guanine
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytosol
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
GUANINE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTidten, N. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Glutamate versus Glutamine Exchange Swaps Substrate Selectivity in tRNA-Guanine Transglycosylase: Insight into the Regulation of Substrate Selectivity by Kinetic and Crystallographic Studies.
Authors: Tidten, N. / Stengl, B. / Heine, A. / Garcia, G.A. / Klebe, G. / Reuter, K.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 6, 2013Group: Other
Revision 1.3Apr 24, 2013Group: Refinement description
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999sequence There is a Thr -> Lys sequence conflict at residue 312 in the Uniprot database.

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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)43,78610
Polymers42,9251
Non-polymers8619
Water1,54986
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,57220
Polymers85,8492
Non-polymers1,72218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7020 Å2
ΔGint-24 kcal/mol
Surface area24450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.144, 63.692, 71.101
Angle α, β, γ (deg.)90.00, 92.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42924.719 Da / Num. of mol.: 1 / Mutation: E235Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
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-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 90611 / % possible obs: 97.6 % / Redundancy: 2.5 % / Rsym value: 0.038 / Net I/σ(I): 21

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1P0B

1p0b


Resolution: 1.8→50 Å
RfactorNum. reflectionSelection details
Rfree0.2858 -random
Rwork0.2187 --
obs0.2187 90611 -
all-90611 -
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 54 86 2828

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