Structure of PDB 3vk8 Chain A Binding Site BS02

Receptor Information

>3vk8 Chain A (length=288) Species: 212035 (Acanthamoeba polyphaga mimivirus)

PQGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLK
VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLS
FDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIK
KYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIEN
LWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFL
VYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLE

Ligand information

>3vk8 Chain D (length=13)

cgtccatgtctac

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vk8 Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Q3 E6 K60 G83 L84 R114 F116 G172 N173 Y174 G220 Y221 Y253 R254 N275 R277 T278 Y280
• Binding residue (residue number reindexed from 1): Q2 E5 K59 G82 L83 R113 F115 G171 N172 Y173 G219 Y220 Y252 R253 N274 R276 T277 Y279

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: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:3vk8, PDBe:3vk8, PDBj:3vk8
• PDBsum: 3vk8
• PubMed: 22170059
• UniProt: Q5UQ00|FPG_MIMIV Probable formamidopyrimidine-DNA glycosylase (Gene Name=MIMI_L315)