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- PDB-6scx: Crystal structure of the catalytic domain of human NUDT12 in comp... -

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Basic information

Entry
Database: PDB / ID: 6scx
TitleCrystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate
ComponentsPeroxisomal NADH pyrophosphatase NUDT12
KeywordsHYDROLASE / NUDIX protein / DENADDING enzyme
Function / homology
Function and homology information


NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / mRNA methylguanosine-cap decapping / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / NAD-cap decapping / NAD catabolic process / NAD biosynthesis via nicotinamide riboside salvage pathway ...NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / mRNA methylguanosine-cap decapping / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / NAD-cap decapping / NAD catabolic process / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NADH metabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisomal matrix / circadian regulation of gene expression / peroxisome / magnesium ion binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
NADH pyrophosphatase-like, N-terminal / NADH pyrophosphatase-like rudimentary NUDIX domain / Zinc ribbon, NADH pyrophosphatase / : / NADH pyrophosphatase zinc ribbon domain / : / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. ...NADH pyrophosphatase-like, N-terminal / NADH pyrophosphatase-like rudimentary NUDIX domain / Zinc ribbon, NADH pyrophosphatase / : / NADH pyrophosphatase zinc ribbon domain / : / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
: / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / NAD-capped RNA hydrolase NUDT12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsMcCarthy, A.A. / Chen, K.M. / Wu, H. / Li, L. / Homolka, D. / Gos, P. / Fleury-Olela, F. / Pillai, R.S.
CitationJournal: Cell Rep / Year: 2019
Title: Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs.
Authors: Wu, H. / Li, L. / Chen, K.M. / Homolka, D. / Gos, P. / Fleury-Olela, F. / McCarthy, A.A. / Pillai, R.S.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal NADH pyrophosphatase NUDT12
B: Peroxisomal NADH pyrophosphatase NUDT12
C: Peroxisomal NADH pyrophosphatase NUDT12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,62915
Polymers120,0033
Non-polymers2,62612
Water724
1
A: Peroxisomal NADH pyrophosphatase NUDT12
B: Peroxisomal NADH pyrophosphatase NUDT12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,86511
Polymers80,0022
Non-polymers1,8639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-54 kcal/mol
Surface area28960 Å2
MethodPISA
2
C: Peroxisomal NADH pyrophosphatase NUDT12
hetero molecules

C: Peroxisomal NADH pyrophosphatase NUDT12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5288
Polymers80,0022
Non-polymers1,5266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-11
Buried area6870 Å2
ΔGint-48 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.859, 229.859, 159.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Peroxisomal NADH pyrophosphatase NUDT12 / Nucleoside diphosphate-linked moiety X motif 12 / Nudix motif 12


Mass: 40000.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT12 / Plasmid: pETM-11-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BQG2, NAD+ diphosphatase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.19 % / Description: Long rods
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.3
Details: 20% (w/v) PEG 3350 0.2M potassium citrate tribasic monohydrate 0.02M CdCl(2) 0.02M m7GTP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.0077 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2019 / Details: Toroidal mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0077 Å / Relative weight: 1
ReflectionResolution: 2.9→114.93 Å / Num. obs: 21142 / % possible obs: 95.8 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.039 / Rrim(I) all: 0.124 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→3.2 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1057 / CC1/2: 0.633 / Rpim(I) all: 0.51 / Rrim(I) all: 1.56 / % possible all: 88.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
Coot0.8.9.2model building
PHASER2.8.2phasing
pointless1.11.21data scaling
XDSMar 15, 2019data reduction
autoPROC1.0.5data scaling
STARANISO2.2.19data scaling
MxCuBEv2data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O3P

6o3p


Resolution: 2.92→114.93 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.863 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.525
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1062 5.02 %RANDOM
Rwork0.232 ---
obs0.233 21142 60.2 %-
Displacement parametersBiso max: 258.63 Å2 / Biso mean: 94.16 Å2 / Biso min: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.8037 Å20 Å20 Å2
2---1.8037 Å20 Å2
3---3.6075 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: final / Resolution: 2.92→114.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7556 0 207 4 7767
Biso mean--80.07 46.34 -
Num. residues----976
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2675SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1402HARMONIC5
X-RAY DIFFRACTIONt_it7948HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1039SEMIHARMONIC5
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_contact8775SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7948HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg10860HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion19.16
LS refinement shellResolution: 2.92→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2914 26 6.15 %
Rwork0.2887 397 -
all0.2889 423 -
obs--8.36 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-37.068223.2226-37.1947
2-28.352533.6592-16.1882
3-42.50817.1121-69.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A115 - 459
2X-RAY DIFFRACTION2{ B|* }B115 - 459
3X-RAY DIFFRACTION3{ C|* }C115 - 459

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