Structure of PDB 3aal Chain A

Receptor sequence

>3aalA (length=298) Species: 1462 (Geobacillus kaustophilus)

LKIGSHVSMSGKKMLLAASEEAASYGANTFMIYTGAPQNTKRKSIEELNI
EAGRQHMQAHGIEEIVVHAPYIINIGNTTNLDTFSLGVDFLRAEIERTEA
IGAKQLVLHPGAHVGAGVEAGLRQIIRGLNEVLTREQNVQIALETMAGKG
SECGRTFEELAYIIDGVAYNDKLSVCFDTCHTHDAGYDIVNDFDGVLEEF
DRIIGLGRLKVLHINDSKNPRGSRKDRHENIGFGHIGFAALNYIVHHPQL
EDIPKILETPYVGEDKNNKKPPYKHEIAMLRAQSFDDQLLEKINAGAE

3D structure

• PDB: 3aal An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA
• Chain: A
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Q39 H69 Y72 H110 E145 D179 H182 H214 D227 H229 E259
• Catalytic site (residue number reindexed from 1): Q38 H68 Y71 H109 E144 D178 H181 H213 D226 H228 E258
• Enzyme Commision number: 3.1.21.2: deoxyribonuclease IV.

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	FE	A	H69 H110 E145	H68 H109 E144
BS02	FE	A	E145 D179 H214 E259	E144 D178 H213 E258
BS03	ZN	A	H182 D227 H229	H181 D226 H228

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008270 zinc ion binding
• GO:0008833 deoxyribonuclease IV (phage-T4-induced) activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:3aal, PDBe:3aal, PDBj:3aal
• PDBsum: 3aal
• PubMed: 21358045
• UniProt: Q5KX27|END4_GEOKA Probable endonuclease 4 (Gene Name=nfo)