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

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Basic information

Entry
Database: PDB / ID: 6eza
TitleCrystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K 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 / cytoplasm / cytosol
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 / 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. / Pecqueur, L. / 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
B: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,54716
Polymers73,6112
Non-polymers1,93614
Water6,467359
1
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7178
Polymers36,8051
Non-polymers9127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8308
Polymers36,8051
Non-polymers1,0257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.470, 77.110, 84.480
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 36805.426 Da / Num. of mol.: 2
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 , 5 types, 373 molecules

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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
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: 0.980035 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980035 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 37936 / % possible obs: 93.1 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.17 / Net I/σ(I): 8
Reflection shellResolution: 2→2.097 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 759 / CC1/2: 0.517 / Rrim(I) all: 1.424 / % possible all: 93.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20170615data reduction
STARANISO1.10.15data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XP7

4xp7


Resolution: 2→38.55 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.242 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1904 5.02 %RANDOM
Rwork0.191 ---
obs0.193 37935 78.3 %-
Displacement parametersBiso mean: 33.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.0347 Å20 Å2-5.4854 Å2
2--6.9765 Å20 Å2
3----8.0111 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 116 359 5280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015017HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066816HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1754SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes893HARMONIC5
X-RAY DIFFRACTIONt_it5017HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion16.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion679SEMIHARMONIC5
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_contact5948SEMIHARMONIC4
LS refinement shellResolution: 2→2.04 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.277 -4.22 %
Rwork0.2148 727 -
all0.2173 759 -
obs--25.41 %
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)
11.1805-0.00210.66520.69640.07882.0587-0.0098-0.07730.04770.0973-0.00180.006-0.0487-0.16530.0116-0.0562-0.013-0.0568-0.00680.0043-0.2105-12.3675-17.9923-8.1818
20.92190.1033-0.40790.8592-0.00691.7276-0.0241-0.0178-0.0435-0.00860.04230.04880.0038-0.1021-0.0181-0.06720.0231-0.0790.00290.0104-0.1903-11.4743-54.6979-34.976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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