3D27

E. coli methionine aminopeptidase with Fe inhibitor W29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of inhibitors of Escherichia coli methionine aminopeptidase with the Fe(II)-form selectivity and antibacterial activity.

Wang, W.L.Chai, S.C.Huang, M.He, H.Z.Hurley, T.D.Ye, Q.Z.

(2008) J.Med.Chem. 51: 6110-6120

  • DOI: 10.1021/jm8005788

  • PubMed Abstract: 
  • Methionine aminopeptidase (MetAP) is a promising target to develop novel antibiotics, because all bacteria express MetAP from a single gene that carries out the essential function of removing N-terminal methionine from nascent proteins. Divalent meta ...

    Methionine aminopeptidase (MetAP) is a promising target to develop novel antibiotics, because all bacteria express MetAP from a single gene that carries out the essential function of removing N-terminal methionine from nascent proteins. Divalent metal ions play a critical role in the catalysis, and there is an urgent need to define the actual metal used by MetAP in bacterial cells. By high throughput screening, we identified a novel class of catechol-containing MetAP inhibitors that display selectivity for the Fe(II)-form of MetAP. X-ray structure revealed that the inhibitor binds to MetAP at the active site with the catechol coordinating to the metal ions. Importantly, some of the inhibitors showed antibacterial activity at low micromolar concentration on Gram-positive and Gram-negative bacteria. Our data indicate that Fe(II) is the likely metal used by MetAP in the cellular environment, and MetAP inhibitors need to inhibit this metalloform of MetAP effectively to be therapeutically useful.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase
A
261Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: map
EC: 3.4.11.18
Find proteins for P0AE18 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE18
Small Molecules
Ligands 2 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
W29
Query on W29

Download SDF File 
Download CCD File 
A
4-(3-ethylthiophen-2-yl)benzene-1,2-diol
C12 H12 O2 S
VXLXQOMDQVQQLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
W29IC50: 55700 nM BINDINGMOAD
W29IC50: 55700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.510α = 90.00
b = 59.880β = 106.47
c = 54.880γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance