- PDB-8ftj: Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosy... -
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Basic information
Entry
Database: PDB / ID: 8ftj
Title
Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosylase bound to DNA duplex containing urea
Components
DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3')
DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3')
Endonuclease 8-like 1
Keywords
DNA BINDING PROTEIN/DNA / base-excision repair enzyme / DNA glycosylase / DNA binding protein / DNA binding protein-DNA complex
Function / homology
Function and homology information
negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function
Endonuclease8-like1 / DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease ...DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease VIII-like 1 / FPG1 / Nei homolog 1 / NEH1 / Nei-like protein 1
Mass: 33641.414 Da / Num. of mol.: 1 / Mutation: P2G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEIL1 / Production host: Escherichia coli (E. coli) References: UniProt: Q96FI4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
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DNA chain , 2 types, 2 molecules DF
#2: DNA chain
DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3')
Mass: 3838.506 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: YB9 is modeled into the chain D of DNA template strand at position 297; basically urea moiety is covalently linked to ring-opened deoxyribose in YB9 residue ie. YB9 is modified nucleotide in ...Details: YB9 is modeled into the chain D of DNA template strand at position 297; basically urea moiety is covalently linked to ring-opened deoxyribose in YB9 residue ie. YB9 is modified nucleotide in DNA template strand (Chain D) Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3')
Mass: 4040.647 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Complementary DNA strand (Chain F) to template strand (chain D) Source: (synth.) synthetic construct (others)
Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
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Details
Has ligand of interest
Y
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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal grow
Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.01 M magnesium sulfate and 1.8 M lithium sulfate, 0.05 M sodium cacodylate, pH 6.0
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
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