Structure of PDB 2f5s Chain A Binding Site BS02

Receptor Information

>2f5s Chain A (length=273) Species: 1422 (Geobacillus stearothermophilus)

PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQT
VRGLERRGKFLKFLLDRDALISHLRMEGRYAVASALEPLEPHTHVVFCFT
DGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAER
AVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIE
RLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLYVYGRQGNPCKR
CGTPIEKTVVAGRGTHYCPRCQR

Ligand information

>2f5s Chain C (length=11)

gtccgagtcta

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2f5s Structure of a DNA glycosylase searching for lesions.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): P2 Q3 E6 K60 H74 R76 M77 R112 G173 N174 I175 S220 T221 V222 R223 T224 Y225 Y242 K258 R264
• Binding residue (residue number reindexed from 1): P1 Q2 E5 K59 H73 R75 M76 R111 G172 N173 I174 S219 T220 V221 R222 T223 Y224 Y241 K257 R263

Enzymatic activity

• Enzyme Commision number: 3.2.2.23: DNA-formamidopyrimidine glycosylase.
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0008270 zinc ion binding
• GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
• GO:0016787 hydrolase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0016829 lyase activity
• GO:0019104 DNA N-glycosylase activity
• GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
• GO:0046872 metal ion binding
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:2f5s, PDBe:2f5s, PDBj:2f5s
• PDBsum: 2f5s
• PubMed: 16497933
• UniProt: P84131