Structure of PDB 1kfv Chain B

Receptor sequence
>1kfvB (length=260) Species: 1358 (Lactococcus lactis) [Search protein sequence]
GELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQ
GISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFAD
GQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLR
KSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLL
HDSIIEILQKAIKLGGSGKMQNELQVYGKTGEKCSRCGAEIQKIKVAGRG
THFCPVCQQK
3D structure
PDB1kfv Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
ChainB
Resolution2.55 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G1
Catalytic site (residue number reindexed from 1) G1
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 B G1 E2 K57 H72 R74 M75 R109 K129 G170 N171 Y238 K254 K256 R260 G1 E2 K57 H72 R74 M75 R109 K129 G170 N171 Y227 K243 K245 R249 PDBbind-CN: Kd=6nM
BS02 dna B H91 V108 R109 K110 F111 H91 V108 R109 K110 F111 PDBbind-CN: Kd=6nM
BS03 ZN B C245 C248 C265 C268 C234 C237 C254 C257
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:1kfv, PDBe:1kfv, PDBj:1kfv
PDBsum1kfv
PubMed12065399
UniProtP42371|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)

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