Structure of PDB 1tdz Chain A Binding Site BS02

Receptor Information

>1tdz Chain A (length=265) Species: 1358 (Lactococcus lactis)

ELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQG
ISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFADG
QLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRK
STKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLH
DSIIEILQKAIKLGGSSILGSTGKMQNELQVYGKTGEKCSRCGAEIQKIK
VAGRGTHFCPVCQQK

Ligand information

>1tdz Chain C (length=14)

gcgagaaacaaaga

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1tdz Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): K90 H91 V108 R109 K110 F111 K154
• Binding residue (residue number reindexed from 1): K89 H90 V107 R108 K109 F110 K153
• Binding affinity: PDBbind-CN: Kd=3nM

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:1tdz, PDBe:1tdz, PDBj:1tdz
• PDBsum: 1tdz
• PubMed: 15249553
• UniProt: P42371|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)