Structure of PDB 4pdi Chain A

Receptor sequence

>4pdiA (length=268) Species: 1359 (Lactococcus cremoris) [Search protein sequence]

PELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQ
GISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFAD
GQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLR
KSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLL
HDSIIEILQKAIKLGGSSIRALGSTGKMQNELQVYGKTGEKCSRCGAEIQ
KIKVAGRGTHFCPVCQQK

3D structure

PDB

4pdi Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.

Chain

Resolution

2.1 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)
BS01	dna	A	P1 E2 E5 K57 H72 R74 M75 E76 R109 K129 Q163 G170 N171 I172 S217 I219 Y238 K254 K256 R260	P1 E2 E5 K57 H72 R74 M75 E76 R109 K129 Q163 G170 N171 I172 S217 I219 Y235 K251 K253 R257
BS02	dna	A	K90 H91 V108 R109 K110 F111	K90 H91 V108 R109 K110 F111
BS03	2ON	A	W179 K182 C268	W179 K182 C265

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

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:4pdi, PDBe:4pdi, PDBj:4pdi
PDBsum	4pdi
PubMed	25143530
UniProt	P42371\|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)

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