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- PDB-6ili: Crystal structure of human MTH1(G2K/D120N mutant) in complex with... -

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Basic information

Entry
Database: PDB / ID: 6ili
TitleCrystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 6.5
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / ALPHA-BETA-ALPHA SANDWICH / DNA DAMAGE / DNA REPAIR / DNA REPLICATION
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsNakamura, T. / Waz, S. / Hirata, K. / Nakabeppu, Y. / Yamagata, Y.
Citation
Journal: J. Biol. Chem. / Year: 2017
Title: Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity
Authors: Waz, S. / Nakamura, T. / Hirata, K. / Koga-Ogawa, Y. / Chirifu, M. / Arimori, T. / Tamada, T. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and preliminary X-ray analysis of human MTH1 with a homogeneous N-terminus.
Authors: Koga, Y. / Inazato, M. / Nakamura, T. / Hashikawa, C. / Chirifu, M. / Michi, A. / Yamashita, T. / Toma, S. / Kuniyasu, A. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionOct 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 7,8-dihydro-8-oxoguanine triphosphatase
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1324
Polymers36,0852
Non-polymers1,0462
Water5,837324
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5662
Polymers18,0431
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-3 kcal/mol
Surface area8480 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5662
Polymers18,0431
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint0 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.071, 47.132, 123.032
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 7,8-dihydro-8-oxoguanine triphosphatase / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18042.605 Da / Num. of mol.: 2 / Mutation: G2K, D120N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: SODIUM CITRATE, cacodylate, NACL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 48166 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 46
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 2390

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→37.413 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.12
RfactorNum. reflection% reflection
Rfree0.2047 2433 5.06 %
Rwork0.1745 --
obs0.176 48102 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→37.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 64 324 2930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132878
X-RAY DIFFRACTIONf_angle_d1.4663928
X-RAY DIFFRACTIONf_dihedral_angle_d17.0771092
X-RAY DIFFRACTIONf_chiral_restr0.102406
X-RAY DIFFRACTIONf_plane_restr0.01504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4487-1.47830.28171370.2162538X-RAY DIFFRACTION95
1.4783-1.51040.27451510.20032608X-RAY DIFFRACTION99
1.5104-1.54560.21991370.18932656X-RAY DIFFRACTION99
1.5456-1.58420.20961390.19012674X-RAY DIFFRACTION99
1.5842-1.62710.24571570.17912623X-RAY DIFFRACTION99
1.6271-1.67490.23841240.18932678X-RAY DIFFRACTION99
1.6749-1.7290.20851310.1822686X-RAY DIFFRACTION100
1.729-1.79080.24491260.18392674X-RAY DIFFRACTION100
1.7908-1.86250.20351550.18812662X-RAY DIFFRACTION100
1.8625-1.94720.21441480.17942693X-RAY DIFFRACTION100
1.9472-2.04990.1961440.17512700X-RAY DIFFRACTION100
2.0499-2.17830.21391630.17252662X-RAY DIFFRACTION100
2.1783-2.34650.21761670.17892701X-RAY DIFFRACTION100
2.3465-2.58260.20021440.18452715X-RAY DIFFRACTION100
2.5826-2.95610.2261420.18272747X-RAY DIFFRACTION100
2.9561-3.72390.17571180.15142799X-RAY DIFFRACTION100
3.7239-37.42560.17581500.16592853X-RAY DIFFRACTION97
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)
12.2705-1.06180.75911.61450.52381.2608-0.01290.15920.2091-0.2917-0.04430.06510.05060.04950.10870.11080.01550.01120.11590.01450.09063.092-0.6462-15.8387
22.99721.23540.00512.1982-0.2443.8183-0.1887-0.07490.25070.11350.17640.3731-0.3937-0.46470.05680.19230.03170.01370.13290.00520.1329-6.3353-17.1632-16.2127
33.4413-0.08-0.53376.54-0.29040.8430.0136-0.24950.04130.91440.01960.2364-0.27270.02270.01030.24190.01180.0180.1353-0.0050.09791.5175-8.0757-5.4106
41.61270.8773-1.17642.4698-1.88621.3930.1203-0.2502-0.18530.2103-0.3813-0.10760.01750.43230.26030.20520.02540.00270.18350.00620.13525.3551-9.9658-13.8194
51.713-0.60681.152.5642-2.09921.98990.06120.0057-0.03470.0709-0.194-0.08580.08280.03770.07620.15280.02190.00590.1299-0.00950.12022.338-2.992-17.834
65.5459-3.06730.64536.8586-1.61983.4227-0.1279-0.90840.62090.44830.1196-0.1943-0.6313-0.02190.20440.34730.0015-0.01390.1559-0.02020.1307-3.758-20.9644-5.4514
71.1627-1.06340.38393.2837-0.7661.8144-0.0414-0.02550.07430.08070.08740.0635-0.1417-0.2285-0.05610.13730.00790.01260.1040.01090.1115-5.0382-21.2608-19.9861
83.2261-1.66060.15942.57160.23671.64010.0573-0.1384-0.20550.11930.06890.18470.1404-0.178-0.15150.204-0.02770.0190.11780.01270.1633.7379-15.3819-24.8179
94.2023-2.68351.5853.8304-0.75252.2452-0.142-0.13340.06640.2170.1339-0.10850.0660.08340.02770.11380.00220.02010.0816-0.00130.08085.8451-7.5664-26.7545
108.25330.2638-2.31710.59790.26641.2339-0.02350.01250.0978-0.00290.01350.06250.0433-0.1367-0.02010.10520.0034-0.01390.1350.00220.09911.47848.0883-14.2159
112.5738-1.3466-0.50266.94990.91062.90230.10560.1888-0.0382-0.1066-0.10350.1784-0.0896-0.1875-0.03190.07770.00650.02260.11520.02660.079332.772513.4069-16.0279
120.609-0.1032-0.90990.8636-0.36495.10430.36511.0419-0.1104-0.76250.14750.4991-0.9344-2.4184-0.29050.38440.21120.01830.58460.11280.241922.001123.0248-13.9764
135.62991.72332.0477.02623.00524.3467-0.3270.94890.0406-0.55350.24090.49530.0468-0.40960.13130.1415-0.0708-0.01390.33070.03140.169515.27979.2826-24.0188
146.65493.12220.47994.0384-0.94830.5422-0.68881.25440.8949-0.41040.33220.10340.3368-0.7059-0.22450.1546-0.05660.03890.44240.00120.152622.69429.7046-26.0708
153.0102-0.6827-1.50272.7620.38281.2453-0.190.0501-0.1638-0.06940.1089-0.02020.00490.07550.08080.1080.0115-0.02530.1486-0.00030.08517.8226.6485-14.4846
164.7012-0.3891-0.69075.84640.7372.5926-0.31960.17180.02420.10820.56350.2427-0.279-0.74290.10310.19940.09230.02790.260.07610.121530.568315.2848-25.4009
175.1692-1.3476-0.43921.9667-0.18992.79550.0968-0.06130.1464-0.0586-0.06530.0401-0.2367-0.09960.00240.1230.01240.00740.09750.00430.113531.639617.0506-11.3778
182.5037-1.7383-0.06863.002-1.721.68210.0189-0.05410.07350.338-0.0836-0.1878-0.42410.27310.020.1208-0.1023-0.03710.30520.08710.155125.99457.8325-5.9609
196.0207-3.3-2.53184.45661.70523.09420.15810.2636-0.1133-0.0509-0.3129-0.0731-0.24760.1280.02360.07420.001-0.00650.1530.04580.079619.66965.1096-5.5132
204.2214-2.2152-1.19992.87570.41332.46280.07060.1414-0.1898-0.2715-0.16850.3431-0.04960.18550.10710.15710.0176-0.01820.1470.02260.079417.68345.5568-2.9675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 88 )
6X-RAY DIFFRACTION6chain 'A' and (resid 89 through 100 )
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 117 )
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 128 )
9X-RAY DIFFRACTION9chain 'A' and (resid 129 through 156 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 11 )
11X-RAY DIFFRACTION11chain 'B' and (resid 12 through 23 )
12X-RAY DIFFRACTION12chain 'B' and (resid 24 through 33 )
13X-RAY DIFFRACTION13chain 'B' and (resid 34 through 44 )
14X-RAY DIFFRACTION14chain 'B' and (resid 45 through 59 )
15X-RAY DIFFRACTION15chain 'B' and (resid 60 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 100 )
17X-RAY DIFFRACTION17chain 'B' and (resid 101 through 117 )
18X-RAY DIFFRACTION18chain 'B' and (resid 118 through 128 )
19X-RAY DIFFRACTION19chain 'B' and (resid 129 through 140 )
20X-RAY DIFFRACTION20chain 'B' and (resid 141 through 156 )

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