Structure of PDB 4nid Chain A

Receptor sequence

>4nidA (length=203) Species: 562 (Escherichia coli)

QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAM
TNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPD
FQPDACLINRYAPGAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKR
NDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQ
AGK

3D structure

• PDB: 4nid Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues.
• Chain: A
• Resolution: 1.58 Å

Enzymatic activity

• Enzyme Commision number: 1.14.11.33: DNA oxidative demethylase.

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	T51 P52 G53 Y55 M57 W69 Y76 K127 L128 C129 H131	T40 P41 G42 Y44 M46 W58 Y65 K116 L117 C118 H120
BS02	dna	A	R161 R167	R150 R156
BS03	MN	A	H131 D133 H187	H120 D122 H176
BS04	AKG	A	N120 Y122 L128 H131 H187 I189 R204 N206	N109 Y111 L117 H120 H176 I178 R193 N195

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008198 ferrous iron binding
• GO:0035515 oxidative RNA demethylase activity
• GO:0035516 broad specificity oxidative DNA demethylase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0006281 DNA repair
• GO:0006307 DNA alkylation repair
• GO:0035513 oxidative RNA demethylation
• GO:0042245 RNA repair
• GO:0070989 oxidative demethylation
• GO:0072702 response to methyl methanesulfonate

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4nid, PDBe:4nid, PDBj:4nid
• PDBsum: 4nid
• PubMed: 24596302
• UniProt: P05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)