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- PDB-4e2v: tRNA-guanine transglycosylase Y106F, C158V mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 4e2v
TitletRNA-guanine transglycosylase Y106F, C158V mutant in complex with preQ1
ComponentsQueuine tRNA-ribosyltransferase
Keywordstransferase/transferase inhibitor / substrate specificity / bacterial TGT / guanin / tRNA / preQ1 / guanine exchange enzyme / transferase-transferase inhibitor complex
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) 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
7-DEAZA-7-AMINOMETHYL-GUANINE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsSchmidt, I. / Reuter, K. / Klebe, G. / Heine, A. / Tidten, N.
CitationJournal: Plos One / Year: 2013
Title: Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor.
Authors: Biela, I. / Tidten-Luksch, N. / Immekus, F. / Glinca, S. / Nguyen, T.X. / Gerber, H.D. / Heine, A. / Klebe, G. / Reuter, K.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5197
Polymers42,9061
Non-polymers6136
Water8,359464
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,03714
Polymers85,8112
Non-polymers1,22612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5700 Å2
ΔGint-12 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.363, 64.894, 70.375
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

21A-893-

HOH

31A-946-

HOH

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Components

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


Mass: 42905.691 Da / Num. of mol.: 1 / Mutation: Y106F, C158V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt, ZMO0363 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT UNP SEQUENCE IS INCORRECT AT THE INDICATED POSITION IN REMARK SEQADV

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM TRIS, 1 mM DTT, 10 % DMSO, 12 % PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2010 / Details: mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.18→30 Å / Num. all: 125858 / Num. obs: 125858 / % possible obs: 95 % / Redundancy: 2.5 % / Biso Wilson estimate: 10.42 Å2 / Net I/σ(I): 21.4
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.13 / Num. unique all: 5750 / Rsym value: 0.218 / % possible all: 88

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GEV

3gev
PDB Unreleased entry


Resolution: 1.18→21.031 Å / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: R_free / σ(F): 1 / Phase error: 11.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1528 12053 9.95 %Random,10%
Rwork0.1375 ---
obs0.1391 121156 91.49 %-
all-121156 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.159 Å2 / ksol: 0.511 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1179 Å2-0 Å2-5.0946 Å2
2---0.5328 Å2-0 Å2
3---0.4149 Å2
Refinement stepCycle: LAST / Resolution: 1.18→21.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 38 464 3312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073047
X-RAY DIFFRACTIONf_angle_d1.2024131
X-RAY DIFFRACTIONf_dihedral_angle_d12.6431154
X-RAY DIFFRACTIONf_chiral_restr0.076431
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1804-1.19380.20153760.16863062X-RAY DIFFRACTION79
1.1938-1.20790.183930.15653309X-RAY DIFFRACTION84
1.2079-1.22260.16123780.15253329X-RAY DIFFRACTION85
1.2226-1.23810.1623730.14683426X-RAY DIFFRACTION86
1.2381-1.25440.16173540.1373440X-RAY DIFFRACTION86
1.2544-1.27160.16844130.1323418X-RAY DIFFRACTION87
1.2716-1.28970.14123780.12663512X-RAY DIFFRACTION88
1.2897-1.3090.14564070.1163519X-RAY DIFFRACTION89
1.309-1.32940.1473860.11583608X-RAY DIFFRACTION90
1.3294-1.35120.13293560.11033663X-RAY DIFFRACTION91
1.3512-1.37450.12044140.10933522X-RAY DIFFRACTION90
1.3745-1.39950.13074070.10843624X-RAY DIFFRACTION92
1.3995-1.42640.12553830.10373706X-RAY DIFFRACTION92
1.4264-1.45550.12854380.10583698X-RAY DIFFRACTION93
1.4555-1.48720.12314130.09983629X-RAY DIFFRACTION93
1.4872-1.52170.12814250.09933706X-RAY DIFFRACTION94
1.5217-1.55980.12344410.10173766X-RAY DIFFRACTION95
1.5598-1.6020.12694010.10043806X-RAY DIFFRACTION96
1.602-1.64910.11994200.10363802X-RAY DIFFRACTION96
1.6491-1.70230.13844270.10813812X-RAY DIFFRACTION96
1.7023-1.76310.13644130.11553835X-RAY DIFFRACTION97
1.7631-1.83360.13683970.12043881X-RAY DIFFRACTION97
1.8336-1.9170.13974070.12533926X-RAY DIFFRACTION97
1.917-2.0180.14874430.13233821X-RAY DIFFRACTION97
2.018-2.14440.15694340.14013944X-RAY DIFFRACTION98
2.1444-2.30970.15834170.13953917X-RAY DIFFRACTION98
2.3097-2.54180.15554230.14253962X-RAY DIFFRACTION99
2.5418-2.90880.15274370.15333966X-RAY DIFFRACTION99
2.9088-3.66160.15363870.15643732X-RAY DIFFRACTION93
3.6616-21.03440.22693120.20822762X-RAY DIFFRACTION68

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