4NIH

Crystal structure of AlkB E136L mutant protein with cofactors bound to dsDNA containing m6A/A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.374 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1002/anie.201310050
  • Primary Citation of Related Structures:  4NID, 4NIG, 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. Swa ...

    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).




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-ketoglutarate-dependent dioxygenase AlkB
A
205Escherichia coli (strain K12)Gene Names: alkB (aidD)
EC: 1.14.11.33
Find proteins for P05050 (Escherichia coli (strain K12))
Go to UniProtKB:  P05050
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'B13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'C13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
B
DNA LINKINGC11 H16 N5 O6 PA
2YR
Query on 2YR
B
NON-POLYMERC11 H18 N3 O7 P S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.374 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.072α = 90.00
b = 76.369β = 108.98
c = 53.178γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Non-polymer description, Structure summary