4KM3

Discovery of a novel structural motif in methionine aminopeptidase from Streptococci with possible post-translational modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

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Literature

Discovery of a new genetic variant of methionine aminopeptidase from streptococci with possible post-translational modifications: biochemical and structural characterization.

Arya, T.Kishor, C.Saddanapu, V.Reddi, R.Addlagatta, A.

(2013) PLoS One 8: e75207-e75207

  • DOI: 10.1371/journal.pone.0075207
  • Primary Citation of Related Structures:  
    4KM3

  • PubMed Abstract: 
  • Protein N-terminal methionine excision is an essential co-translational process that occurs in the cytoplasm of all organisms. About 60-70% of the newly synthesized proteins undergo this modification. Enzyme responsible for the removal of initiator m ...

    Protein N-terminal methionine excision is an essential co-translational process that occurs in the cytoplasm of all organisms. About 60-70% of the newly synthesized proteins undergo this modification. Enzyme responsible for the removal of initiator methionine is methionine aminopeptidase (MetAP), which is a dinuclear metalloprotease. This protein is conserved through all forms of life from bacteria to human except viruses. MetAP is classified into two isoforms, Type I and II. Removal of the map gene or chemical inhibition is lethal to bacteria and to human cell lines, suggesting that MetAP could be a good drug target. In the present study we describe the discovery of a new genetic variant of the Type I MetAP that is present predominantly in the streptococci bacteria. There are two inserts (insert one: 27 amino acids and insert two: four residues) within the catalytic domain. Possible glycosylation and phosphorylation posttranslational modification sites are identified in the 'insert one'. Biochemical characterization suggests that this enzyme behaves similar to other MetAPs in terms of substrate specificity. Crystal structure Type Ia MetAP from Streptococcus pneumoniae (SpMetAP1a) revealed that it contains two molecules in the asymmetric unit and well ordered inserts with structural features that corroborate the possible posttranslational modification. Both the new inserts found in the SpMetAP1a structurally align with the P-X-X-P motif found in the M. tuberculosis and human Type I MetAPs as well as the 60 amino acid insert in the human Type II enzyme suggesting possible common function. In addition, one of the β-hairpins within in the catalytic domain undergoes a flip placing a residue which is essential for enzyme activity away from the active site and the β-hairpin loop of this secondary structure in the active site obstructing substrate binding. This is the first example of a MetAP crystallizing in the inactive form.


    Organizational Affiliation

    Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine aminopeptidaseAB286Streptococcus pneumoniae CGSP14Mutation(s): 0 
Gene Names: mapSPCG_1194
EC: 3.4.11.18
Find proteins for B2IQ22 (Streptococcus pneumoniae (strain CGSP14))
Explore B2IQ22 
Go to UniProtKB:  B2IQ22
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.687α = 90
b = 109.687β = 90
c = 164.424γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Data collection