Structure of PDB 3gpu Chain A Binding Site BS02

Receptor Information

>3gpu Chain A (length=251) Species: 1422 (Geobacillus stearothermophilus)

PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQT
VRGLERRGKFLKFLLDRDALISHLRMEGRYAVASALEPLEPHTHVVFCFT
DGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAER
AVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIE
RLHEEMVATIGEAVMLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQ
R

Ligand information

>3gpu Chain C (length=12)

gtccgagtctac

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gpu Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
• Resolution: 1.62 Å
• Binding residue (original residue number in PDB): K60 H74 R76 F114 P129 P130 N174 R264 G265
• Binding residue (residue number reindexed from 1): K59 H73 R75 F113 P128 P129 N173 R241 G242

Enzymatic activity

• Catalytic site (original residue number in PDB): P2 E3
• Catalytic site (residue number reindexed from 1): P1 E2
• 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:3gpu, PDBe:3gpu, PDBj:3gpu
• PDBsum: 3gpu
• PubMed: 20010681
• UniProt: P84131