4NID

Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A

• PDB DOI: https://doi.org/10.2210/pdb4NID/pdb
• NAKB: 4NID

• Classification: OXIDOREDUCTASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-06 Released: 2014-04-16 
• Deposition Author(s): Zhu, C.X., Yi, C.Q.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.197 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues.

Zhu, C., Yi, C.

(2014) Angew Chem Int Ed Engl 53: 3659-3662

• PubMed: 24596302 
• DOI: https://doi.org/10.1002/anie.201310050
• Primary Citation of Related Structures:  
  4NID, 4NIG, 4NIH, 4NII


• PubMed Abstract: 
  

  The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active-site residues that contribute to their substrate specificity. Swapping such active-site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X-ray structures and enzyme kinetics suggests a role of the active-site residues in substrate recognition. Such a divergent active-site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.

---

Organizational Affiliation: 

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871 (China).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.06 kDa 
• Atom Count: 2,507 
• Modelled Residue Count: 228 
• Deposited Residue Count: 231 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase AlkB	A	205	Escherichia coli	Mutation(s): 1  Gene Names: alkB, aidD, b2212, JW2200 EC: 1.14.11.33
UniProt
Find proteins for P05050 (Escherichia coli (strain K12)) Explore P05050  Go to UniProtKB:  P05050

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'	B	13	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'	C	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	E [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.197 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.416	α = 90
b = 75.907	β = 108.84
c = 52.088	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-16 
Deposition Author(s): Zhu, C.X., Yi, C.Q.

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2014-05-28
  Changes: Non-polymer description, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description