Structure of PDB 6fbu Chain A Binding Site BS02

Receptor Information

>6fbu Chain A (length=254) Species: 83333 (Escherichia coli K-12)

PQGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETR
GKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTI
LLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRN
RQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHA
LLEIPRFSYATRGQALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCP
GCQH

Ligand information

>6fbu Chain C (length=13)

ccaggacgaagcc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fbu Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): P1 Q2 K52 H67 Q69 L70 F121 R124 Q160 N168 Y169 R252 P253
• Binding residue (residue number reindexed from 1): P1 Q2 K52 H67 Q69 L70 F121 R124 Q160 N168 Y169 R244 P245

Enzymatic activity

• Enzyme Commision number: 3.2.2.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
• 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: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: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:6fbu, PDBe:6fbu, PDBj:6fbu
• PDBsum: 6fbu
• UniProt: P50465|END8_ECOLI Endonuclease 8 (Gene Name=nei)