3MAT

E.COLI METHIONINE AMINOPEPTIDASE TRANSITION-STATE INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis.

Lowther, W.T.Orville, A.M.Madden, D.T.Lim, S.Rich, D.H.Matthews, B.W.

(1999) Biochemistry 38: 7678-7688

  • DOI: 10.1021/bi990684r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By improving the expression and purification of Escherichia coli methionine aminopeptidase (eMetAP) and using slightly different crystallization conditions, the resolution of the parent structure was extended from 2.4 to 1.9 A resolution. This has pe ...

    By improving the expression and purification of Escherichia coli methionine aminopeptidase (eMetAP) and using slightly different crystallization conditions, the resolution of the parent structure was extended from 2.4 to 1.9 A resolution. This has permitted visualization of the coordination geometry and solvent structure of the active-site dinuclear metal center. One solvent molecule (likely a mu-hydroxide) bridges the trigonal bipyramidal (Co1) and octahedral (Co2) cobalt ions. A second solvent (possibly a hydroxide ion) is bound terminally to Co2. A monovalent cation binding site was also identified about 13 A away from the metal center at an interface between the two subdomains of the protein. The first structure of a substrate-like inhibitor, (3R)-amino-(2S)-hydroxyheptanoyl-L-Ala-L-Leu-L-Val-L-Phe-OMe, bound to a methionine aminopeptidase, has also been determined. This inhibitor coordinates the metal center through four interactions as follows: (i) ligation of the N-terminal (3R)-nitrogen to Co2, (ii, iii) bridging coordination of the (2S)-hydroxyl group, and (iv) terminal ligation to Co1 by the keto oxygen of the pseudo-peptide linkage. Inhibitor binding occurs with the displacement of two solvent ligands and the expansion of the coordination sphere of Co1. In addition to the tetradentate, bis-chelate metal coordination, the substrate analogue forms hydrogen bonds with His79 and His178, two conserved residues within the active site of all MetAPs. To evaluate their importance in catalysis His79 and His178 were replaced with alanine. Both substitutions, but especially that of His79, reduce activity. The structure of the His79Ala apoenzyme and the comparison of its electronic absorption spectra with other variants suggest that the loss in activity is not due to a conformational change or a defective metal center. Two different reaction mechanisms are proposed and are compared to those of related enzymes. These results also suggest that inhibitors analogous to that reported here may be useful in preventing angiogenesis in cancer and in the treatment of microbial and fungal infections.


    Related Citations: 
    • The Anti-Angiogenic Agent Fumagillin Covalently Modifies a Conserved Active- Site Histidine in the Escherichia Coli Methionine Aminopeptidase
      Lowther, W.T.,Mcmillen, D.A.,Orville, A.M.,Matthews, B.W.
      (1998) Proc.Natl.Acad.Sci.USA 95: 12153
    • Structure of the Cobalt-Dependent Methionine Aminopeptidase from Escherichia Coli: A New Type of Proteolytic Enzyme
      Roderick, S.L.,Matthews, B.W.
      (1993) Biochemistry 32: 3907


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, Department of Physics, University of Oregon, Eugene 97403, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHIONINE AMINOPEPTIDASE
A
265Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: map
EC: 3.4.11.18
Find proteins for P0AE18 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE18
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bestatin-based inhibitor (3R)-amino-(2S)-hydroxyheptanoyl-l-Ala-l-Leu-l-Val-l-Phe-OMe
I
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0A9
Query on 0A9
I
L-PEPTIDE LINKINGC10 H13 N O2PHE
AHH
Query on AHH
I
L-PEPTIDE LINKINGC7 H15 N O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.297α = 90.00
b = 65.155β = 106.12
c = 51.371γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
TNTrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2018-03-14
    Type: Database references