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- PDB-6ezc: Crystal Structure of human tRNA-dihydrouridine(20) synthase catal... -

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Basic information

Entry
Database: PDB / ID: 6ezc
TitleCrystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K double mutant
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsFLAVOPROTEIN / RNA BINDING PROTEIN / TRNA PROCESSING / OXIDOREDUCTASE
Function / homology
Function and homology information


tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / double-stranded RNA binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / double-stranded RNA binding / FMN binding / flavin adenine dinucleotide binding / tRNA binding / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
DUS2, double-stranded RNA binding domain / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / TRIETHYLENE GLYCOL / tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBou-Nader, C. / Bregeon, D. / Vincent, G. / Fontecave, M. / Hamdane, D.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0004-01 France
French National Research AgencyANR-11-LABX-0011-01 France
CitationJournal: Biochemistry / Year: 2018
Title: Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases.
Authors: Bou-Nader, C. / Bregeon, D. / Pecqueur, L. / Fontecave, M. / Hamdane, D.
History
DepositionNov 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

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Assembly

Deposited unit
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,11311
Polymers36,8061
Non-polymers1,30610
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-86 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.990, 84.660, 100.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein tRNA-dihydrouridine(20) synthase [NAD(P)+]-like / Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine ...Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine synthase 2-like / hDUS2


Mass: 36806.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia coli (E. coli) / Variant (production host): pLysS
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 6 types, 240 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% PEG 2000 MME 200 mM ammonium sulfate 50 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980066 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980066 Å / Relative weight: 1
ReflectionResolution: 2→43.17 Å / Num. obs: 22677 / % possible obs: 89.9 % / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.17 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.9 % / Rmerge(I) obs: 2.521 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1135 / CC1/2: 0.413 / Rrim(I) all: 2.665 / % possible all: 43.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20151015data reduction
STARANISO1.10.15data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XP7

4xp7


Resolution: 2→42.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1124 4.96 %RANDOM
Rwork0.182 ---
obs0.184 22658 83.3 %-
Displacement parametersBiso mean: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.6035 Å20 Å20 Å2
2---5.748 Å20 Å2
3---5.1444 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 79 230 2677
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033360HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d871SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes435HARMONIC5
X-RAY DIFFRACTIONt_it2481HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion16.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion332SEMIHARMONIC5
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_contact3088SEMIHARMONIC4
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2 -5.07 %
Rwork0.2182 431 -
all0.2174 454 -
obs--20.78 %
Refinement TLS params.Method: refined / Origin x: 19.7569 Å / Origin y: -1.8799 Å / Origin z: -12.6109 Å
111213212223313233
T-0.0196 Å2-0.0174 Å2-0.0126 Å2--0.0655 Å2-0.0044 Å2--0.0624 Å2
L0.7668 °20.2619 °2-0.2993 °2-1.4383 °2-0.5718 °2--1.2257 °2
S0.0315 Å °-0.0644 Å °0.0516 Å °0.054 Å °-0.0293 Å °0.0387 Å °-0.0291 Å °0.0188 Å °-0.0022 Å °
Refinement TLS groupSelection details: { A|* }

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