- PDB-2oxm: Crystal structure of a UNG2/modified DNA complex that represent a... -
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Basic information
Entry
Database: PDB / ID: 2oxm
Title
Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping
Components
DNA (5'-D(*AP*AP*AP*GP*AP*TP*(4MF)P*AP*CP*A)-3')
DNA (5'-D(*TP*GP*TP*TP*AP*TP*CP*TP*T)-3')
Uracil-DNA glycosylase
Keywords
Hydrolase/DNA / ENZYME DNA COMPLEX / UNG2 / URACIL DNA GLYCOSYLASE / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information
base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus Similarity search - Function
Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: A solution of human UNG2 (22 mg/ml) in 50 mM Tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M duplex DNA (2.5 mM)m incubate at room Temperature for 30 min. and then ...Details: A solution of human UNG2 (22 mg/ml) in 50 mM Tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M duplex DNA (2.5 mM)m incubate at room Temperature for 30 min. and then centrifugate at 10000 g for 5 min.Co-crystallizarion condition were 22% PEG 4000, 100 MM HEPES pH 6.5 and 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
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