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- PDB-8uuc: Crystal structure of a bacterial clusterless MutYX bound to an Ab... -

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Basic information

Entry
Database: PDB / ID: 8uuc
TitleCrystal structure of a bacterial clusterless MutYX bound to an Abasic site analog (THF) opposite d(8-oxo-G)
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')
KeywordsDNA BINDING PROTEIN/DNA / DNA glycosylase / Base Excision Repair / DNA-protein complex / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / 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
Similarity search - Function
Endonuclease III-like, conserved site-2 / Endonuclease III family signature. / Adenine/Thymine-DNA glycosylase / Helix-hairpin-helix motif / 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
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesEggerthella sp. YY7918 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTrasvina-Arenas, C.H. / David, S.S. / Fisher, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204228 United States
CitationJournal: Biorxiv / Year: 2025
Title: Crystal structure of MutYX: A novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-Oxoguanine recognition sphere.
Authors: Trasvina-Arenas, C.H. / Hashemian, M. / Malek, M. / Merrill, S. / Fisher, A.J. / David, S.S.
History
DepositionNov 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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)38,23021
Polymers37,2603
Non-polymers97018
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-30 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.832, 84.137, 225.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#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


Mass: 30645.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eggerthella sp. YY7918 (bacteria) / Strain: YY7918 / Gene: MutY / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: F7V0V1

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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 / 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 / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 287 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.29 % / Description: long needle-like crystal
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM CAPS/Sodium hydroxide [pH 10.5], 1200 mM Sodium phosphate monobasic/800 mM Potassium phosphate dibasic, and 200 mM Lithium sulfate
PH range: 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2022
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 53001 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 12.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.525 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2535 / CC1/2: 0.739 / Rpim(I) all: 0.607 / Rrim(I) all: 1.643 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→37.62 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.6434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 5122 5.1 %
Rwork0.1762 95302 -
obs0.1773 53001 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.41 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 438 58 269 2906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692780
X-RAY DIFFRACTIONf_angle_d1.03533847
X-RAY DIFFRACTIONf_chiral_restr0.0504416
X-RAY DIFFRACTIONf_plane_restr0.0103430
X-RAY DIFFRACTIONf_dihedral_angle_d22.793549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.40791710.35543107X-RAY DIFFRACTION96.7
1.57-1.590.38051430.35073183X-RAY DIFFRACTION96.07
1.59-1.610.35831780.31773161X-RAY DIFFRACTION95.73
1.61-1.630.34971430.31823204X-RAY DIFFRACTION96.87
1.63-1.650.30211730.30653144X-RAY DIFFRACTION96.54
1.65-1.670.31471650.28513136X-RAY DIFFRACTION95.52
1.67-1.690.29091870.27963147X-RAY DIFFRACTION96.05
1.69-1.720.28331690.27983265X-RAY DIFFRACTION97.95
1.72-1.750.31611390.26613081X-RAY DIFFRACTION94.82
1.75-1.770.2981850.26043096X-RAY DIFFRACTION93.96
1.77-1.80.26831570.23052950X-RAY DIFFRACTION91.65
1.8-1.840.21791870.22553184X-RAY DIFFRACTION95.2
1.84-1.870.22861530.20823210X-RAY DIFFRACTION98.25
1.87-1.910.24461640.19653197X-RAY DIFFRACTION97.62
1.91-1.950.23012050.19373135X-RAY DIFFRACTION96.25
1.95-20.20551650.19453278X-RAY DIFFRACTION99.48
2-2.050.22861870.18923106X-RAY DIFFRACTION95.34
2.05-2.10.23851770.18133282X-RAY DIFFRACTION99.86
2.1-2.170.24331830.18253135X-RAY DIFFRACTION96.06
2.17-2.240.17581740.17293258X-RAY DIFFRACTION99.85
2.24-2.320.21741670.1733207X-RAY DIFFRACTION96.34
2.32-2.410.1921640.17423192X-RAY DIFFRACTION97.59
2.41-2.520.21651450.16993061X-RAY DIFFRACTION94.13
2.52-2.650.19131830.16693206X-RAY DIFFRACTION97.33
2.65-2.820.22831910.18083208X-RAY DIFFRACTION98.66
2.82-3.030.17931820.17063255X-RAY DIFFRACTION98.96
3.03-3.340.16441730.15323244X-RAY DIFFRACTION98.87
3.34-3.820.1611870.14593251X-RAY DIFFRACTION98.91
3.82-4.810.14431770.13373148X-RAY DIFFRACTION96.32
4.81-37.620.16911480.15893271X-RAY DIFFRACTION98.9
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)
11.42825259018-0.3547851932460.6488103753331.08861019717-0.6129143380063.364348514717.78191468811E-50.119698726317-0.0454118040999-0.0851788115363-0.02459294522380.02792136378620.1934461922490.07336426259230.01803139182660.1740970211360.01274448508920.01228165886930.17065429305-0.005094759349030.2200331025226.28213.48318.341
24.55089412622-0.5678837134360.5052133888943.402142534310.6182367492956.16457865667-0.00738780535651-0.2608374903990.08580142836390.369104831516-0.0399198166827-0.0370758588271-0.2395710995210.2716674584350.06421333910610.263338915251-0.01042025060060.02014331214950.2187735143010.00506394926050.1510538609545.87621.14847.748
38.11439057039-6.093880281030.8386961070667.01166329613-0.7259337356774.38118239752-0.380767281465-1.1006413521-1.96155060534-0.2148941186390.468055622593-1.61227610929-0.107204333963-0.208677808201-0.07342020465930.292641302088-0.06574630513790.01610750406770.776387891842-0.1551556887160.790703552526-13.08219.0627.379
42.950291031792.230762259022.957811376494.99378296294-0.6230546124545.6639901356-0.10672625223-0.3656640542970.285462102975-0.186060299083-0.1129661416910.27563133531-0.270404283102-0.3115084535810.1779955503140.2408286506550.0755291234837-0.01338569456440.179733386804-0.02716577546850.2403159869713.5224.21131.903
52.00011853539-6.91463492837-3.380212260284.712052104632.602970190196.266779814711.6616488759-0.790945907385.76198358185-0.947609480070.332033177489-3.21014105872-5.317379368192.51955404447-1.961730003411.0464531825-0.2019797993530.2055719888240.691062793839-0.1071264243981.2173622963510.88841.05827.936
64.462879277043.9162661232-0.6907214603718.40463333438-1.20974761152.052154018290.020442948889-0.09412237676460.163991247718-0.0248261105072-0.02712584413070.226376325562-0.219754794628-0.03761822652290.01315476340790.1874161046820.0455585796246-0.01091385482210.182612055940.005769834175230.1679480602413.24925.82824.343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:198 )A1 - 198
2X-RAY DIFFRACTION2( CHAIN A AND RESID 199:273 )A199 - 273
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:2 )B1 - 2
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:9 )B3 - 9
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:2 )C1 - 2
6X-RAY DIFFRACTION6( CHAIN C AND RESID 3:9 )C3 - 9

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