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- PDB-9bs2: Glycosylase MutY variant R149Q in complex with DNA containing d(8... -

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Basic information

Entry
Database: PDB / ID: 9bs2
TitleGlycosylase MutY variant R149Q in complex with DNA containing d(8-oxo-G) paired with a product analog (THF) to 1.51 A resolution
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
KeywordsHYDROLASE/DNA / Protein-DNA complex / DNA repair / Base Excision Repair / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / 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 ...A/G-specific adenine glycosylase MutY / 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-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsTrasvina-Arenas, C.H. / Tamayo, N. / Lin, W.J. / Demir, M. / Fisher, A.J. / David, S.S. / Horvath, M.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2204228 United States
National Science Foundation (NSF, United States)2204229 United States
National Science Foundation (NSF, United States)1905249 United States
National Science Foundation (NSF, United States)1905304 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair.
Authors: Trasvina-Arenas, C.H. / Dissanayake, U.C. / Tamayo, N. / Hashemian, M. / Lin, W.J. / Demir, M. / Hoyos-Gonzalez, N. / Fisher, A.J. / Cisneros, G.A. / Horvath, M.P. / David, S.S.
History
DepositionMay 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2108
Polymers48,6783
Non-polymers5325
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-72 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.500, 86.000, 140.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase / oxoG:A-specific adenine glycosylase


Mass: 42063.836 Da / Num. of mol.: 1 / Mutation: R149Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mutY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P83847, adenine glycosylase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')


Mass: 3423.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')


Mass: 3191.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 246 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.9 % / Description: large 0.2 x 0.3 mm
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 14%, 0.4 M calcium acetate, 2% ethylene glycol, pH 8.5, with microseed crystals from N146S 10X stock

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2021
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.51→70.3 Å / Num. obs: 136096 / % possible obs: 98.7 % / Redundancy: 4.86 % / Biso Wilson estimate: 25.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.061 / Net I/σ(I): 12.2
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 3.37 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 0.51 / Num. unique obs: 9284 / CC1/2: 0.124 / Rrim(I) all: 2.56 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→43 Å / SU ML: 0.2895 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 3412 2.52 %Random selection
Rwork0.2059 132132 --
obs0.2065 135544 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.81 Å2
Refinement stepCycle: LAST / Resolution: 1.51→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 422 15 241 3377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01193361
X-RAY DIFFRACTIONf_angle_d1.17944697
X-RAY DIFFRACTIONf_chiral_restr0.0618526
X-RAY DIFFRACTIONf_plane_restr0.0106533
X-RAY DIFFRACTIONf_dihedral_angle_d18.1571239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.43841210.42884514X-RAY DIFFRACTION81.59
1.53-1.550.39291360.41575210X-RAY DIFFRACTION92.03
1.55-1.580.41291390.38315397X-RAY DIFFRACTION96.95
1.58-1.60.41241370.36865549X-RAY DIFFRACTION99.04
1.6-1.630.38121450.35445471X-RAY DIFFRACTION96.58
1.63-1.660.32741470.33135514X-RAY DIFFRACTION99.37
1.66-1.690.36211390.31325554X-RAY DIFFRACTION98.49
1.69-1.730.32271440.28445520X-RAY DIFFRACTION98.49
1.73-1.770.29561510.27555553X-RAY DIFFRACTION99.86
1.77-1.810.29331390.2695556X-RAY DIFFRACTION98.97
1.81-1.850.27891510.25795585X-RAY DIFFRACTION99.97
1.85-1.90.31400.26995587X-RAY DIFFRACTION99.39
1.9-1.960.37651430.28035619X-RAY DIFFRACTION99.91
1.96-2.020.25251380.24115543X-RAY DIFFRACTION99.7
2.02-2.090.24241510.23755618X-RAY DIFFRACTION99.57
2.09-2.180.24911410.22015586X-RAY DIFFRACTION99.88
2.18-2.280.26081570.22385583X-RAY DIFFRACTION99.74
2.28-2.40.20151540.21885554X-RAY DIFFRACTION99.84
2.4-2.550.24121450.21225614X-RAY DIFFRACTION99.93
2.55-2.740.21861480.2115619X-RAY DIFFRACTION99.97
2.74-3.020.20611410.20085555X-RAY DIFFRACTION99.65
3.02-3.460.20721370.17595647X-RAY DIFFRACTION99.91
3.46-4.350.20561280.14685570X-RAY DIFFRACTION99.82
4.35-430.15981400.16485614X-RAY DIFFRACTION99.86
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)
14.09275858623-0.458857627026-0.4401091414191.32328701526-0.2990128029690.9285967081450.216982998990.8516739148560.0799945509503-0.184851868973-0.143048493413-0.01538257754-0.0418512001529-0.02964916062080.07368621871860.1694759425890.05097976362980.01268100358890.2414147973780.02693474969460.13273382791512.47645920112.232613459812.49912094515
20.469837340031-0.07883501731220.237230029460.448815433226-0.03142654954320.356071351835-0.0144984594669-0.3957717638310.2230982266930.284031518630.156605487256-0.2575834926040.02777945139010.3152365368580.006746511648890.375098228610.0146571898637-0.03171821889820.488838513002-0.1081792309390.24703980550420.64503193577.7615972218637.1948197687
30.394835755466-0.3241947780920.131029341650.4075391751970.0152030404460.1618347710950.0319240020446-0.277029067298-0.174842541243-0.135566307639-0.0938301922943-0.06003182249270.329000303390.16099243658-7.59036304751E-50.2834907460980.02592951389230.01080240056420.2143738444470.04231320964540.25849025462319.68878154-4.1257637460116.2188716829
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and (resid 8:228))AA8 - 2281 - 221
22(chain A and (resid 229:360 or resid 402 or resid 405))AA - F229 - 405222
33((chain B and resid 1:11) or (chain C and resid 12:22))B - CG - H1 - 22

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