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- PDB-9nzd: Crystal structure of AfNth1-K122A mutant bound to Tg-DNA duplex c... -

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Basic information

Entry
Database: PDB / ID: 9nzd
TitleCrystal structure of AfNth1-K122A mutant bound to Tg-DNA duplex complex in an intermediate state
Components
  • DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')
  • DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')
  • Endonuclease III
KeywordsLYASE/DNA / DNA-glycosylase / AP-lyase / hydrolase / LYASE-DNA complex
Function / homology
Function and homology information


G/T mismatch-specific thymine-DNA glycosylase activity / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / nucleotide-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
Endonuclease III / Iron-sulfur binding domain of endonuclease III / 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 ...Endonuclease III / Iron-sulfur binding domain of endonuclease III / 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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Endonuclease III
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHitomi, K. / Arvai, A.S. / Syed, A. / Parikh, S. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
CitationJournal: Nat Commun / Year: 2026
Title: A unified catalytic mechanism in bifunctional DNA glycosylases with an evolutionarily conserved aspartate-lysine dyad.
Authors: Syed, A. / Serafim, L.F. / Arvai, A.S. / Minko, I.G. / Tang, H.Y.H. / Huffman, J.L. / Mol, C.D. / Hitomi, K. / Sarker, A.H. / Parikh, S. / Tsai, C.L. / Bacolla, A. / Shin, D.S. / Cunningham, ...Authors: Syed, A. / Serafim, L.F. / Arvai, A.S. / Minko, I.G. / Tang, H.Y.H. / Huffman, J.L. / Mol, C.D. / Hitomi, K. / Sarker, A.H. / Parikh, S. / Tsai, C.L. / Bacolla, A. / Shin, D.S. / Cunningham, R.P. / Iwai, S. / Chowdhury, D. / Lloyd, R.S. / Ivanov, I. / Tainer, J.A.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease III
B: DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')
C: DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')
D: Endonuclease III
E: DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9618
Polymers63,2586
Non-polymers7032
Water27015
1
A: Endonuclease III
B: DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')
C: DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9814
Polymers31,6293
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-29 kcal/mol
Surface area13830 Å2
MethodPISA
2
D: Endonuclease III
E: DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9814
Polymers31,6293
Non-polymers3521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-34 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.247, 110.247, 112.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Endonuclease III / DNA-(apurinic or apyrimidinic site) lyase


Mass: 23650.746 Da / Num. of mol.: 2 / Mutation: K122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: nth, AF_1692 / Production host: Escherichia coli (E. coli)
References: UniProt: O28581, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')


Mass: 3979.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG8000, 100 mM imidazole/malonate, pH 4.5-5.5, 5 mM DTT, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→38.98 Å / Num. obs: 13134 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.2
Reflection shellResolution: 3.1→3.32 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.306 / Num. unique obs: 2321 / CC1/2: 0.839 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→38.98 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 35.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 616 5.13 %
Rwork0.2136 --
obs0.2163 12018 91.57 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 1058 0 15 4342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044525
X-RAY DIFFRACTIONf_angle_d0.7086355
X-RAY DIFFRACTIONf_dihedral_angle_d21.7411835
X-RAY DIFFRACTIONf_chiral_restr0.043726
X-RAY DIFFRACTIONf_plane_restr0.018626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.38141230.31572375X-RAY DIFFRACTION78
3.41-3.910.32591490.27242829X-RAY DIFFRACTION92
3.91-4.920.27461690.23352982X-RAY DIFFRACTION96
4.92-38.980.23021750.17443216X-RAY DIFFRACTION99

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