Structure of PDB 3a46 Chain A

Receptor sequence
>3a46A (length=288) Species: 212035 (Acanthamoeba polyphaga mimivirus) [Search protein sequence]
PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLK
VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLS
FDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIK
KYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIEN
LWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFL
VYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLE
3D structure
PDB3a46 Structural Characterization of a Viral NEIL1 Ortholog Unliganded and Bound to Abasic Site-containing DNA
ChainA
Resolution2.2 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.2.2.23: DNA-formamidopyrimidine glycosylase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna A Y95 M113 R114 F116 S272 G273 K274 N275 Y94 M112 R113 F115 S271 G272 K273 N274 PDBbind-CN: Kd=47pM
BS02 dna A E3 K60 G83 L84 R114 F116 G172 N173 Y221 Y253 R254 N275 R277 T278 Y280 E2 K59 G82 L83 R113 F115 G171 N172 Y220 Y252 R253 N274 R276 T277 Y279 PDBbind-CN: Kd=47pM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3a46, PDBe:3a46, PDBj:3a46
PDBsum3a46
PubMed19625256
UniProtQ5UQ00|FPG_MIMIV Probable formamidopyrimidine-DNA glycosylase (Gene Name=MIMI_L315)

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