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- PDB-5mp0: Human m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 5mp0
TitleHuman m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain
Componentsm7GpppN-mRNA hydrolase
KeywordsHYDROLASE / mRNA decapping / Nudix
Function / homology
Function and homology information


exoribonuclease activity, producing 5'-phosphomonoesters / regulation of telomerase RNA localization to Cajal body / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / mRNA decay by 5' to 3' exoribonuclease / 5'-3' exoribonuclease activity / exonucleolytic catabolism of deadenylated mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / m7G(5')pppN diphosphatase activity / histone mRNA catabolic process ...exoribonuclease activity, producing 5'-phosphomonoesters / regulation of telomerase RNA localization to Cajal body / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / mRNA decay by 5' to 3' exoribonuclease / 5'-3' exoribonuclease activity / exonucleolytic catabolism of deadenylated mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / m7G(5')pppN diphosphatase activity / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / telomerase RNA binding / RISC complex / negative regulation of telomere maintenance via telomerase / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / mRNA catabolic process / regulation of mRNA stability / P-body / cytoplasmic ribonucleoprotein granule / cell junction / manganese ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping protein 2, Box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain ...Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping protein 2, Box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / NUDIX hydrolase domain / Nudix hydrolase domain profile. / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMathea, S. / Salah, E. / Velupillai, S. / Tallant, C. / Pike, A.C.W. / Bushell, S.R. / Faust, B. / Wang, D. / Burgess-Brown, N. / von Delft, F. ...Mathea, S. / Salah, E. / Velupillai, S. / Tallant, C. / Pike, A.C.W. / Bushell, S.R. / Faust, B. / Wang, D. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Huber, K.
CitationJournal: To Be Published
Title: Human m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain
Authors: Mathea, S. / Huber, K.
History
DepositionDec 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: m7GpppN-mRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1113
Polymers18,9871
Non-polymers1242
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.050, 60.570, 65.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein m7GpppN-mRNA hydrolase / / Nucleoside diphosphate-linked moiety X motif 20 / Nudix motif 20 / mRNA-decapping enzyme 2 / hDpc


Mass: 18986.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCP2, NUDT20 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8IU60, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M acetate pH 4.5 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.63→38.73 Å / Num. obs: 24476 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rrim(I) all: 0.088 / Net I/σ(I): 11.3
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.8 / Rrim(I) all: 1.895 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j3t
Resolution: 1.63→38.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.585 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26178 1244 5.1 %RANDOM
Rwork0.21187 ---
obs0.21441 23182 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.885 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å2-0 Å2
2---2.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.63→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 8 60 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191216
X-RAY DIFFRACTIONr_bond_other_d0.0020.021134
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9671651
X-RAY DIFFRACTIONr_angle_other_deg1.08432604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88723.51954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.225158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211370
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0072.969600
X-RAY DIFFRACTIONr_mcbond_other2.9892.963599
X-RAY DIFFRACTIONr_mcangle_it4.0734.435750
X-RAY DIFFRACTIONr_mcangle_other4.074.444751
X-RAY DIFFRACTIONr_scbond_it3.9983.297616
X-RAY DIFFRACTIONr_scbond_other3.9733.296616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8514.802902
X-RAY DIFFRACTIONr_long_range_B_refined7.06224.1961330
X-RAY DIFFRACTIONr_long_range_B_other7.07524.2131331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 96 -
Rwork0.342 1672 -
obs--99.44 %

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