E. coli methionine aminopeptidase unliganded, 1:0.5

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.227 

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This is version 1.4 of the entry. See complete history


Structural basis of catalysis by monometalated methionine aminopeptidase.

Ye, Q.Z.Xie, S.X.Ma, Z.Q.Huang, M.Hanzlik, R.P.

(2006) Proc Natl Acad Sci U S A 103: 9470-9475

  • DOI: https://doi.org/10.1073/pnas.0602433103
  • Primary Citation of Related Structures:  
    2GTX, 2GU4, 2GU5, 2GU6, 2GU7

  • PubMed Abstract: 

    Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of Escherichia coli MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.

  • Organizational Affiliation

    High Throughput Screening Laboratory and Department of Medicinal Chemistry, University of Kansas, 1501 Wakarusa Drive, Lawrence, KS 66045, USA. qye@ku.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase
A, B
263Escherichia coliMutation(s): 1 
Gene Names: map
Find proteins for P0AE18 (Escherichia coli (strain K12))
Explore P0AE18 
Go to UniProtKB:  P0AE18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE18
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.2α = 90
b = 61.98β = 107.36
c = 77.05γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2006-07-04 
  • Deposition Author(s): Ye, Q.Z.

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description