Structure of PDB 4pd2 Chain A

Receptor sequence
>4pd2A (length=272) Species: 1359 (Lactococcus cremoris) [Search protein sequence]
PELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQ
GISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFAD
GQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLR
KSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLL
HDSIIEILQKAIKLGGSSIRTYSALGSTGKMQNELQVYGKTGEKCSRGHG
AEIQKIKVAGRGTHFCPVCQQK
3D structure
PDB4pd2 Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
ChainA
Resolution1.65 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) P1 E2
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.
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 E2 K57 H72 R74 M75 Q163 G170 N171 Y238 K255 R261 E2 K57 H72 R74 M75 Q163 G170 N171 Y238 K255 R261
BS02 dna A K90 H91 V108 R109 F111 K90 H91 V108 R109 F111
BS03 ZN A C245 H249 C266 C269 C245 H249 C266 C269
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4pd2, PDBe:4pd2, PDBj:4pd2
PDBsum4pd2
PubMed25143530
UniProtP42371|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)

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