Structure of PDB 3bie Chain A

Receptor sequence

>3bieA (length=202) Species: 83333 (Escherichia coli K-12)

EPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMT
NCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDF
QPDACLINRYAPGAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRN
DPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQA
GK

3D structure

• PDB: 3bie Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA
• Chain: A
• Resolution: 1.68 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 G75 Y76 K127 L128 C129 H131 R210	T39 P40 G41 Y43 M45 W57 G63 Y64 K115 L116 C117 H119 R198
BS02	dna	A	R161 N162 R167	R149 N150 R155
BS03	MN	A	H131 D133 H187	H119 D121 H175
BS04	AKG	A	N120 Y122 L128 H131 H187 I189 R204 N206 R210	N108 Y110 L116 H119 H175 I177 R192 N194 R198

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:3bie, PDBe:3bie, PDBj:3bie
• PDBsum: 3bie
• PubMed: 18432238
• UniProt: P05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)