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- PDB-7ef9: Crystal structure of mouse MUTYH in complex with DNA containing A... -

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Basic information

Entry
Database: PDB / ID: 7ef9
TitleCrystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form II)
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / adenine glycosylase / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / negative regulation of necroptotic process / oxidized purine DNA binding ...adenine/guanine mispair binding / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / adenine glycosylase / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / negative regulation of necroptotic process / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / response to oxidative stress / DNA repair / mitochondrion / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif ...Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsNakamura, T. / Nakabeppu, Y. / Yamagata, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Authors: Nakamura, T. / Okabe, K. / Hirayama, S. / Chirifu, M. / Ikemizu, S. / Morioka, H. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionMar 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine DNA glycosylase
B: DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3')
C: DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,66412
Polymers58,5783
Non-polymers1,0869
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-135 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.660, 108.496, 158.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase / MutY homolog / mMYH


Mass: 50109.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mutyh, Myh / Production host: Escherichia coli (E. coli) / References: UniProt: Q99P21, adenine glycosylase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3')


Mass: 4385.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3')


Mass: 4082.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 244 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350, lithium sulfate, ammonium sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→42.53 Å / Num. obs: 43985 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.92 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 33.1
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.576 / Num. unique obs: 2188

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→42.53 Å / SU ML: 0.2275 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.9545 / Stereochemistry target values: GeoSDT + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1972 2222 5.05 %
Rwork0.1778 41752 -
obs0.1788 43974 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.03 Å2
Refinement stepCycle: LAST / Resolution: 1.97→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 540 45 235 4075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634033
X-RAY DIFFRACTIONf_angle_d0.83225619
X-RAY DIFFRACTIONf_chiral_restr0.0497611
X-RAY DIFFRACTIONf_plane_restr0.0048633
X-RAY DIFFRACTIONf_dihedral_angle_d18.82341506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.30851390.26072517X-RAY DIFFRACTION96.37
2.01-2.060.25351290.23172580X-RAY DIFFRACTION99.01
2.06-2.110.25161190.21582569X-RAY DIFFRACTION99.04
2.11-2.160.24641210.20642589X-RAY DIFFRACTION98.8
2.16-2.230.25511390.19252587X-RAY DIFFRACTION99.16
2.23-2.30.22991420.1872565X-RAY DIFFRACTION99.19
2.3-2.380.22021450.18682593X-RAY DIFFRACTION99.24
2.38-2.480.24541520.18122576X-RAY DIFFRACTION99.27
2.48-2.590.24381400.18282584X-RAY DIFFRACTION99.42
2.59-2.730.21841370.19512605X-RAY DIFFRACTION99.42
2.73-2.90.22341410.19812620X-RAY DIFFRACTION99.5
2.9-3.120.21031330.1972638X-RAY DIFFRACTION99.64
3.12-3.430.18711260.18252647X-RAY DIFFRACTION99.78
3.43-3.930.17381340.16742653X-RAY DIFFRACTION99.86
3.93-4.950.15571700.14582646X-RAY DIFFRACTION99.89
4.95-42.530.19571550.17392783X-RAY DIFFRACTION99.53
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)
12.13917398468-0.4371836521540.0232013085364.43383592822-0.8141709250771.435319900250.12606771056-0.08117941133660.00555663243540.1565213412660.03066597485270.0126851816919-0.161184944136-0.11088000163-0.1590884373430.28996350149-0.03179100973190.05119204545040.321967115233-0.05357228507110.28510984231474.077476717815.692048938831.5636660304
21.313352233530.694947936471-1.810034088441.22769585352-1.155194898544.750915291050.103638511410.2313321139290.041558478645-0.164590432783-0.119443727775-0.422061095232-0.1498086338850.4657811045420.01664268544840.342005541382-0.03097752690940.08516362846850.533442486162-0.04778666052570.55975536335101.89261639816.963676408420.6626438061
33.60171866647-0.523385279522-0.8953301589222.797256977550.1429476878014.585606410740.2719746148230.4856378340950.430430312387-0.4521452862773.40849193277E-50.134787571849-0.6387860194-0.348050939944-0.2242476961920.4647091969580.0993064869920.09091195194980.3485737771710.07596742470050.35793371490960.801422250540.724282461316.8158049851
43.012719272752.059448485141.527086218797.52066700289-0.6974004612356.421718171620.4291578146890.5575881135530.0137765131288-0.3621291532820.0787156866235-1.616354148950.5853884901110.871816160665-0.2950111737160.5027084964540.0712872962630.1220989915370.534651035913-0.07031880326510.69006020612782.04436540527.139835013415.3420202482
53.26779943470.15100948762-0.2658566250221.91580740257-2.002492069534.96948400769-0.07398437092380.3576549586271.29092681128-1.02706548907-0.2701872843050.16095059244-0.7621411894870.1837328555770.3825951699130.715053087824-0.05422680090360.05492717452980.4404236890670.06056412937230.75990062513983.19399327428.088502118815.987368439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 86:200 )
2X-RAY DIFFRACTION2chain 'A' and ((resid 52:79) or (resid 201:331))
3X-RAY DIFFRACTION3chain 'A' and (resid 332:470)
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 14 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 13 )

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