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- PDB-3gp1: MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in E... -

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Basic information

Entry
Database: PDB / ID: 3gp1
TitleMutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-V222P complex
Components
  • 5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*CP**C)-3'
  • 5'-D(P*TP*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)-3'
  • DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / DNA repair / damage search / base extrusion / disulfide crosslinking / DNA damage / DNA-binding / Glycosidase / Hydrolase / Lyase / Metal-binding / Multifunctional enzyme / Zinc-finger / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSpong, M.C. / Qi, Y. / Verdine, G.L.
CitationJournal: Nature / Year: 2009
Title: Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme
Authors: Qi, Y. / Spong, M.C. / Nam, K. / Banerjee, A. / Jiralerspong, S. / Karplus, M. / Verdine, G.L.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA glycosylase
B: 5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*CP**C)-3'
C: 5'-D(P*TP*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1724
Polymers40,1063
Non-polymers651
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-21.1 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.613, 92.845, 105.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA glycosylase /


Mass: 30581.314 Da / Num. of mol.: 1 / Mutation: Q166C, V222P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: MutM / Plasmid: pET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS
References: UniProt: P84131, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain 5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*CP**C)-3'


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain 5'-D(P*TP*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*CP*C)-3'


Mass: 4576.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE SEQUENCE IN THE UNP DATABASE IS NOT THE WILD-TYPE SEQUENCE, BUT HAS GLU 3 TO ...AUTHORS STATE THAT THE SEQUENCE IN THE UNP DATABASE IS NOT THE WILD-TYPE SEQUENCE, BUT HAS GLU 3 TO GLN 3 MUTATION THAT MAKES THE ENZYME INACTIVE. THE SEQUENCE WITH GLU AT POSITION 3 IS THE WILD-TYPE SEQUENCE.

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, Sodium cacodylate, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Sodium cacodylate11
3Glycerol11
4PEG 800012
5Sodium cacodylate12
6Glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2006
Details: Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes. LN2 cooled first crystal, sagittal focusing 2nd crystal
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 28412 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.138 / Χ2: 1.073 / Net I/σ(I): 11.588
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.125.50.49228071.0551100
2.12-2.215.60.40928091.084199.9
2.21-2.315.70.33128111.0871100
2.31-2.435.70.28428331.0781100
2.43-2.585.80.23928391.0921100
2.58-2.785.80.20128401.06199.9
2.78-3.065.80.16528471.076199.9
3.06-3.515.90.13728951.064199.8
3.51-4.425.80.10428721.065199.1
4.42-505.50.07528591.07192.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F5O

2f5o


Resolution: 2.05→45.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1336 4.9 %RANDOM
Rwork0.188 ---
obs0.189 27498 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.65 Å2 / Biso mean: 32.956 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 533 1 180 2684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222622
X-RAY DIFFRACTIONr_angle_refined_deg1.4822.2363660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.53621.13688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86315344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1341526
X-RAY DIFFRACTIONr_chiral_restr0.0930.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211814
X-RAY DIFFRACTIONr_mcbond_it0.6971.51265
X-RAY DIFFRACTIONr_mcangle_it1.30122044
X-RAY DIFFRACTIONr_scbond_it2.05831357
X-RAY DIFFRACTIONr_scangle_it3.1964.51616
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 80 -
Rwork0.186 1545 -
all-1625 -
obs--91.04 %
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)
10.9761-1.1445-0.69653.41742.51923.1862-0.0001-0.04340.1619-0.048-0.004-0.1548-0.13530.15570.0041-0.0217-0.0467-0.0001-0.0286-0.02520.014323.447-6.2778.51
20.63160.7108-0.08552.0465-0.1790.01710.0719-0.0626-0.16180.0606-0.15340.0460.09680.02010.0815-0.0188-0.00810.00410.0123-0.0017-0.002814.164-24.049.019
31.1632-0.3585-0.81041.53621.17611.31860.0210.03430.0739-0.0981-0.08170.0081-0.1121-0.08460.06080.01650.0138-0.008-0.0158-0.0111-0.006115.241-10.1723.936
41.0607-0.4518-0.81640.58690.10680.7756-0.0562-0.10940.08830.05170.0664-0.05770.06920.106-0.0102-0.00870.01430.00490.0351-0.0248-0.020624.921-17.9113.832
50.7521-0.38071.09731.72850.78992.77940.0588-0.09040.1463-0.1155-0.21780.0970.1465-0.14150.1589-0.0479-0.0150.0010.0266-0.04320.00696.903-12.3948.351
60.2652-0.1823-0.22191.35341.35772.08660.0720.06150.023-0.0448-0.19260.07610.0049-0.08290.1205-0.01320.0415-0.0345-0.0223-0.08750.00585.0757.57922.571
711.6273-5.3438-5.31965.0194.65494.33960.2569-0.24850.2309-0.4538-0.0366-0.2186-0.43390.1418-0.22030.05180.00850.0074-0.0533-0.0344-0.047112.65712.82820.142
82.6483.5892.610.0548-3.07610.9451-0.01880.2296-0.1664-0.26670.2285-0.61510.58130.7377-0.2097-0.00410.06460.0132-0.0035-0.086-0.016620.657.22434.783
91.35850.48631.43862.74910.82371.56040.0822-0.04070.07190.1768-0.17960.12210.1896-0.1010.09740.0396-0.04010.0333-0.0207-0.0716-0.021311.7698.1837.047
105.7106-1.78240.44473.60490.29660.0968-0.5468-0.4527-0.18680.49850.52490.7188-0.01240.31360.0219-0.00010.06340.0889-0.00890.02820.02074.142-12.75828.606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 48
3X-RAY DIFFRACTION3A49 - 73
4X-RAY DIFFRACTION4A74 - 112
5X-RAY DIFFRACTION5A113 - 133
6X-RAY DIFFRACTION6A134 - 198
7X-RAY DIFFRACTION7A199 - 216
8X-RAY DIFFRACTION8A238 - 250
9X-RAY DIFFRACTION9A251 - 274
10X-RAY DIFFRACTION10B1 - 14
11X-RAY DIFFRACTION10C3 - 15

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