1XNZ

Crystal Structure of Mn(II) form of E. coli. Methionine Aminopeptidase in complex with 5-(2-chlorophenyl)furan-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Metalloform-Selective Inhibitors of Escherichia coli Methionine Aminopeptidase and X-ray Structure of a Mn(II)-Form Enzyme Complexed with an Inhibitor.

Ye, Q.-Z.Xie, S.-X.Huang, M.Huang, W.-J.Lu, J.-P.Ma, Z.-Q.

(2004) J Am Chem Soc 126: 13940-13941

  • DOI: 10.1021/ja045864p
  • Primary Citation of Related Structures:  
    1XNZ

  • PubMed Abstract: 
  • Methionine aminopeptidase (MetAP) enzymes require a divalent metal ion such as Mn(II), Fe(II), Co(II), Ni(II), or Zn(II) for its removal of the N-terminal methionine from newly synthesized proteins, but it is not certain which of these ions is most important in vivo ...

    Methionine aminopeptidase (MetAP) enzymes require a divalent metal ion such as Mn(II), Fe(II), Co(II), Ni(II), or Zn(II) for its removal of the N-terminal methionine from newly synthesized proteins, but it is not certain which of these ions is most important in vivo. Metalloform-selective MetAP inhibitors could be valuable for defining which metals are physiologically relevant for MetAP activation and could serve as leads for development of new therapeutic agents. We have screened a library of 43 736 small drug-like molecules against Escherichia coli MetAP and identified two groups of potent and highly metalloform-selective inhibitors of the Co(II)-form, and of the Mn(II)-form, of this enzyme. Compound 1 is 790-fold more selective for the Co(II)-form, while compound 4 is over 640-fold more potent toward the Mn(II)-form. The X-ray structure of a di-Mn(II) form of E. coli MetAP complexed with the Mn(II)-form-selective compound 4 was obtained, and it shows that the inhibitor interacts with both Mn(II) ions through the two oxygen atoms of its free carboxylate group. The preferential coordination of the hard (oxygen) donors to Mn(II) may contribute to its superb selectivity toward the Mn(II)-form.


    Organizational Affiliation

    High Throughput Screening Laboratory and Protein Structure Laboratory, University of Kansas, Lawrence, Kansas 66045, USA. qye@ku.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine aminopeptidaseA264Escherichia coliMutation(s): 0 
Gene Names: map
EC: 3.4.11.18
Find proteins for P0AE18 (Escherichia coli (strain K12))
Explore P0AE18 
Go to UniProtKB:  P0AE18
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FCD
Query on FCD

Download CCD File 
A
5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC ACID
C11 H7 Cl O3
PJGGWIHXGHQXMM-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FCDIC50:  511   nM  BindingDB
FCDIC50:  138000   nM  BindingDB
FCDIC50:  141000   nM  BindingDB
FCDIC50:  200000   nM  BindingDB
FCDIC50:  240   nM  Binding MOAD
FCDIC50:  780   nM  BindingDB
FCDIC50:  116000   nM  BindingDB
FCDIC50 :  240   nM  PDBBind
FCDIC50:  510   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.6α = 90
b = 60.3β = 104.8
c = 49.7γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
XDSdata reduction
AMoREphasing
CNSrefinement
CrystalCleardata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance