2GTX

Structural Basis of Catalysis by Mononuclear Methionine Aminopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.Usa 103: 9470-9475

  • DOI: 10.1073/pnas.0602433103
  • Primary Citation of Related Structures:  

  • 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 meta ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase
A, B
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NLP
Query on NLP

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Download CCD File 
A, B
(1-AMINO-PENTYL)-PHOSPHONIC ACID
NORLEUCINE PHOSPHONATE
C5 H14 N O3 P
NXTPDFMZKSLVRK-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.809α = 90.00
b = 64.257β = 108.09
c = 76.172γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-04-28 
  • Released Date: 2006-07-04 
  • Deposition Author(s): Ye, Q.Z.

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Structure summary