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Basic information

Entry
Database: PDB / ID: 3qi5
TitleCrystal structure of human alkyladenine DNA glycosylase in complex with 3,N4-ethenocystosine containing duplex DNA
Components
  • DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
  • DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')
  • DNA-3-methyladenine glycosylase
KeywordsHYDROLASE/DNA / alkyladenine DNA glycosylase fold / AAG / Excision / DNA repair / DNA binding / Nucleus / HYDROLASE-DNA complex
Function / homology
Function and homology information


alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / DNA alkylation repair / Displacement of DNA glycosylase by APEX1 ...alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / DNA alkylation repair / Displacement of DNA glycosylase by APEX1 / mitochondrial nucleoid / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / base-excision repair / damaged DNA binding / nucleoplasm / cytosol
Similarity search - Function
3-methyladenine DNA Glycosylase; Chain A / Methylpurine-DNA glycosylase (MPG) / Methylpurine-DNA glycosylase / Methylpurine-DNA glycosylase superfamily / Methylpurine-DNA glycosylase (MPG) / Formyl transferase-like, C-terminal domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA-3-methyladenine glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLingaraju, G.M. / Davis, C.A. / Setser, J.W. / Samson, L.D. / Drennan, C.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for the Inhibition of Human Alkyladenine DNA Glycosylase (AAG) by 3,N4-Ethenocytosine-containing DNA.
Authors: Lingaraju, G.M. / Davis, C.A. / Setser, J.W. / Samson, L.D. / Drennan, C.L.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Atomic model
Revision 1.3Sep 13, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-3-methyladenine glycosylase
B: DNA-3-methyladenine glycosylase
C: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
D: DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')
E: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
F: DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6748
Polymers64,5646
Non-polymers1102
Water4,179232
1
A: DNA-3-methyladenine glycosylase
C: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
D: DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3374
Polymers32,2823
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-19 kcal/mol
Surface area12660 Å2
MethodPISA
2
B: DNA-3-methyladenine glycosylase
E: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
F: DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3374
Polymers32,2823
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-19 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.226, 41.220, 82.144
Angle α, β, γ (deg.)81.23, 88.40, 89.15
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUSERSER1AA86 - 1987 - 119
211LEULEUSERSER1BB86 - 1987 - 119
121ASPASPLEULEU1AA211 - 244132 - 165
221ASPASPLEULEU1BB211 - 244132 - 165
131VALVALGLYGLY4AA256 - 263177 - 184
231VALVALGLYGLY4BB256 - 263177 - 184
141PROPROASPASP4AA274 - 289195 - 210
241PROPROASPASP4BB274 - 289195 - 210
112DGDGDTDT4CC1 - 131 - 13
212DGDGDTDT4EE1 - 131 - 13
113DGDGDCDC4DD14 - 251 - 12
213DGDGDCDC4FF14 - 251 - 12

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA-3-methyladenine glycosylase / / 3-alkyladenine DNA glycosylase / 3-methyladenine DNA glycosidase / ADPG / N-methylpurine-DNA glycosylase


Mass: 24314.891 Da / Num. of mol.: 2 / Fragment: delta79AAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPG, AAG, ANPG, MID1 / Plasmid: pET19b-PPS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29372, DNA-3-methyladenine glycosylase II
#2: DNA chain DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')


Mass: 3966.594 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')


Mass: 4000.624 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: The 3,N4-ethenocytosine (EDC) containing DNA duplex was prepared by annealing the EDC containing 13-mer crystallization oligonucleotide ('5-GAC ATG (EDC)TT GCC T-3') with its complementary ...Details: The 3,N4-ethenocytosine (EDC) containing DNA duplex was prepared by annealing the EDC containing 13-mer crystallization oligonucleotide ('5-GAC ATG (EDC)TT GCC T-3') with its complementary strand that contained G opposite EDC (5'-GGC AAG CAT GTC A-3'). The delta79AAG-EDC complexes were prepared by mixing equimolar ratios of delta79AAG and EDC:G 13-mer DNA duplex at the final protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM Hepes-NaOH pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. The crystals were obtained upon mixing 1 uL of complex and 1 ul of the reservoir solution (100 mM sodium cacodylate pH 6.0, 200 mM manganese chloride and 20% polyethylene glycol (PEG)-3350) over 0.5 ml of the reservoir solution, followed by incubation for 2 days, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2006
RadiationMonochromator: Double Crystal, Double Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.2→81.11 Å / Num. all: 26278 / Num. obs: 26278 / % possible obs: 100 %
Reflection shellResolution: 2.2→2.252 Å / % possible all: 89.61

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BNK, used as a search model

1bnk


Resolution: 2.2→81 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.824 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28427 1331 5.1 %RANDOM
Rwork0.23637 ---
obs0.23881 24947 96.22 %-
all-24947 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.29 Å20.21 Å2
2---1.06 Å20.13 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 1024 2 232 4507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224468
X-RAY DIFFRACTIONr_angle_refined_deg1.0292.2696254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7095412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35121.895153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21315563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9881544
X-RAY DIFFRACTIONr_chiral_restr0.0580.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213078
X-RAY DIFFRACTIONr_mcbond_it0.4861.52070
X-RAY DIFFRACTIONr_mcangle_it0.88823310
X-RAY DIFFRACTIONr_scbond_it0.5732398
X-RAY DIFFRACTIONr_scangle_it0.9994.52944
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1152tight positional0.290.05
11B184medium positional0.150.5
22C263medium positional0.330.5
22E245medium positional0.130.5
11A1152tight thermal0.080.5
11B184medium thermal0.072
22D263medium thermal0.142
22F245medium thermal0.12
LS refinement shellResolution: 2.2→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 86 -
Rwork0.289 1734 -
obs--89.61 %
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)
12.1497-1.12670.70342.4143-1.17492.68960.07580.17620.05610.0858-0.1194-0.09370.0805-0.00060.04360.1644-0.0144-0.00170.01890.00310.050319.534410.0103-41.3271
22.3455-1.2472-1.22252.43821.02472.6073-0.14190.1152-0.09610.12840.07910.0643-0.05680.08340.06280.0225-0.02930.00570.2082-0.00120.0578-0.229-9.7377-67.7282
30.3987-0.4108-0.3981.95660.36122.24330.0381-0.0323-0.12670.3619-0.07940.0891-0.08370.01830.04140.2316-0.03480.01080.0233-0.00080.070614.82385.6987-21.1756
41.6315-1.2689-0.91487.54730.51213.33170.0261-0.0565-0.06230.3992-0.2245-0.10750.1154-0.15520.19840.1557-0.0239-0.01340.05240.03050.05915.0784.0514-21.6272
50.34430.26-0.8411.46-0.69712.8385-0.17820.155-0.0593-0.17110.0208-0.00130.1245-0.24730.15740.1656-0.0765-0.00550.2863-0.02150.06624.2907-4.9353-87.7975
69.9932-1.2419-0.53540.8286-1.25792.63520.15260.6552-0.3351-0.023-0.15280.0544-0.01590.10210.00020.084-0.00810.01410.1335-0.03030.09145.9779-5.3712-87.3452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 198
2X-RAY DIFFRACTION1A211 - 244
3X-RAY DIFFRACTION1A256 - 263
4X-RAY DIFFRACTION1A274 - 289
5X-RAY DIFFRACTION2B86 - 198
6X-RAY DIFFRACTION2B211 - 244
7X-RAY DIFFRACTION2B256 - 263
8X-RAY DIFFRACTION2B274 - 289
9X-RAY DIFFRACTION3C1 - 13
10X-RAY DIFFRACTION4D14 - 25
11X-RAY DIFFRACTION5E1 - 13
12X-RAY DIFFRACTION6F14 - 25

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