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- PDB-6o3p: Crystal structure of the catalytic domain of mouse Nudt12 in comp... -

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Basic information

Entry
Database: PDB / ID: 6o3p
TitleCrystal structure of the catalytic domain of mouse Nudt12 in complex with AMP and 3 Mg2+ ions
ComponentsPeroxisomal NADH pyrophosphatase NUDT12
KeywordsHYDROLASE / Nudix protein / deNADding enzyme / Complex
Function / homology
Function and homology information


NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / RNA NAD-cap (NMN-forming) hydrolase activity / NAD-cap decapping / Nicotinamide salvaging / NAD catabolic process / NADH metabolic process / mRNA catabolic process ...NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / RNA NAD-cap (NMN-forming) hydrolase activity / NAD-cap decapping / Nicotinamide salvaging / NAD catabolic process / NADH metabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisome / magnesium ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
NADH pyrophosphatase-like, N-terminal / NADH pyrophosphatase-like rudimentary NUDIX domain / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon domain / Domain of unknown function DUF3447 / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain ...NADH pyrophosphatase-like, N-terminal / NADH pyrophosphatase-like rudimentary NUDIX domain / Zinc ribbon, NADH pyrophosphatase / NADH pyrophosphatase zinc ribbon domain / Domain of unknown function DUF3447 / 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
ADENOSINE MONOPHOSPHATE / NAD-capped RNA hydrolase NUDT12
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTong, L. / Wu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structural and mechanistic basis of mammalian Nudt12 RNA deNADding.
Authors: Grudzien-Nogalska, E. / Wu, Y. / Jiao, X. / Cui, H. / Mateyak, M.K. / Hart, R.P. / Tong, L. / Kiledjian, M.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,45012
Polymers75,4792
Non-polymers97110
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-89 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.207, 58.550, 61.707
Angle α, β, γ (deg.)102.40, 115.19, 104.66
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 37739.258 Da / Num. of mol.: 2 / Mutation: E219A, E220A, E221A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DCN1, NAD+ diphosphatase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 24% (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→52.7 Å / Num. obs: 76455 / % possible obs: 89.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.653

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IW4

5iw4


Resolution: 1.6→52.665 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.26
RfactorNum. reflection% reflection
Rfree0.2189 1999 2.62 %
Rwork0.1799 --
obs0.181 76425 89.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→52.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 0 27 290 5284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155149
X-RAY DIFFRACTIONf_angle_d1.357008
X-RAY DIFFRACTIONf_dihedral_angle_d6.54325
X-RAY DIFFRACTIONf_chiral_restr0.087771
X-RAY DIFFRACTIONf_plane_restr0.01902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5969-1.63680.48021000.38833728X-RAY DIFFRACTION63
1.6368-1.68110.33311350.31875053X-RAY DIFFRACTION86
1.6811-1.73050.29621450.27035513X-RAY DIFFRACTION93
1.7305-1.78640.28141410.24515542X-RAY DIFFRACTION93
1.7864-1.85030.27741590.23015532X-RAY DIFFRACTION93
1.8503-1.92430.31611460.25285235X-RAY DIFFRACTION89
1.9243-2.01190.22371460.18715564X-RAY DIFFRACTION94
2.0119-2.1180.18581470.17615572X-RAY DIFFRACTION94
2.118-2.25070.22471390.18265372X-RAY DIFFRACTION91
2.2507-2.42450.24221440.17565363X-RAY DIFFRACTION91
2.4245-2.66840.21421560.18055584X-RAY DIFFRACTION94
2.6684-3.05450.20691480.18265359X-RAY DIFFRACTION91
3.0545-3.84820.22621490.16565576X-RAY DIFFRACTION94
3.8482-52.69380.17041440.14475433X-RAY DIFFRACTION92
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)
12.2602-0.1627-1.30564.6599-0.87032.88460.02260.1139-0.041-0.27830.0502-0.3582-0.00590.1614-0.03380.2610.03560.06130.2468-0.01710.222817.337331.9814-32.7606
21.1057-0.01160.15471.43690.30995.14150.05230.03980.1406-0.23320.0916-0.1453-0.23880.3736-0.04150.22420.00540.07950.2790.00510.286115.367639.9832-21.8953
31.7257-1.41790.57722.4644-0.94151.97050.10650.01580.1428-0.1463-0.0599-0.0504-0.0646-0.021-0.02930.2275-0.02070.00960.1529-0.00340.1945-5.85449.0211-19.5229
42.8435-1.5535-0.7041.51270.14860.68180.28150.25520.3569-0.5776-0.161-0.2468-0.2972-0.0293-0.10590.42680.03530.03840.23230.04490.2683-9.030755.274-29.5816
51.8655-0.4599-0.74343.7447-0.46383.7651-0.1434-0.22650.05280.27520.20680.181-0.2252-0.2558-0.04230.21020.048-0.00180.2539-0.03070.1888-9.573250.88526.6853
62.46151.161-1.06885.0478-1.32372.0442-0.163-0.5869-0.41420.92610.2064-0.09530.24080.1339-0.00860.42950.09870.00820.45840.06760.3103-6.74639.275811.7013
74.31330.1356-1.82352.0537-0.4882.8320.0155-0.13940.29090.07310.0909-0.2643-0.12840.3263-0.07780.1683-0.0299-0.02130.2066-0.05850.19466.174347.0598-2.7818
80.95590.53330.14443.29290.35590.73530.02140.0242-0.0934-0.261-0.03440.01060.1057-0.00830.01890.22550.0069-0.00980.17680.00510.1701-3.933627.9011-16.793
92.85121.59340.70443.52431.55611.69070.0179-0.0193-0.25850.0923-0.20570.43950.2529-0.24210.19970.2506-0.010.00330.24370.02470.2614-15.600521.2118-12.7858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 123:232 )A123 - 232
2X-RAY DIFFRACTION2( CHAIN A AND RESID 233:307 )A233 - 307
3X-RAY DIFFRACTION3( CHAIN A AND RESID 308:390 )A308 - 390
4X-RAY DIFFRACTION4( CHAIN A AND RESID 391:457 )A391 - 457
5X-RAY DIFFRACTION5( CHAIN B AND RESID 124:225 )B124 - 225
6X-RAY DIFFRACTION6( CHAIN B AND RESID 226:261 )B226 - 261
7X-RAY DIFFRACTION7( CHAIN B AND RESID 262:307 )B262 - 307
8X-RAY DIFFRACTION8( CHAIN B AND RESID 308:417 )B308 - 417
9X-RAY DIFFRACTION9( CHAIN B AND RESID 418:460 )B418 - 460

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