Crystal structure of methionine aminopeptidase from Rickettsia prowazekii bound to methionine

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents.

Helgren, T.R.Chen, C.Wangtrakuldee, P.Edwards, T.E.Staker, B.L.Abendroth, J.Sankaran, B.Housley, N.A.Myler, P.J.Audia, J.P.Horn, J.R.Hagen, T.J.

(2017) Bioorg Med Chem 25: 813-824

  • DOI: https://doi.org/10.1016/j.bmc.2016.11.013
  • Primary Citation of Related Structures:  
    3MR1, 3MX6

  • PubMed Abstract: 

    Methionine aminopeptidase (MetAP) is a class of ubiquitous enzymes essential for the survival of numerous bacterial species. These enzymes are responsible for the cleavage of N-terminal formyl-methionine initiators from nascent proteins to initiate post-translational modifications that are often essential to proper protein function. Thus, inhibition of MetAP activity has been implicated as a novel antibacterial target. We tested this idea in the present study by targeting the MetAP enzyme in the obligate intracellular pathogen Rickettsia prowazekii. We first identified potent RpMetAP inhibitory species by employing an in vitro enzymatic activity assay. The molecular docking program AutoDock was then utilized to compare published crystal structures of inhibited MetAP species to docked poses of RpMetAP. Based on these in silico and in vitro screens, a subset of 17 compounds was tested for inhibition of R. prowazekii growth in a pulmonary vascular endothelial cell (EC) culture infection model system. All compounds were tested over concentration ranges that were determined to be non-toxic to the ECs and 8 of the 17 compounds displayed substantial inhibition of R. prowazekii growth. These data highlight the therapeutic potential for inhibiting RpMetAP as a novel antimicrobial strategy and set the stage for future studies in pre-clinical animal models of infection.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase
A, B
262Rickettsia prowazekiiMutation(s): 0 
Gene Names: mapRP824
Find proteins for Q9ZCD3 (Rickettsia prowazekii (strain Madrid E))
Explore Q9ZCD3 
Go to UniProtKB:  Q9ZCD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZCD3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.37α = 90
b = 67.55β = 97.43
c = 80.89γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-02-08
    Changes: Database references
  • Version 1.3: 2017-02-15
    Changes: Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description