4ZIU

Crystal structure of native alpha-2-macroglobulin from Escherichia coli spanning the residues from domain MG7 to the C-terminus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional insights into Escherichia coli alpha 2-macroglobulin endopeptidase snap-trap inhibition.

Garcia-Ferrer, I.Arede, P.Gomez-Blanco, J.Luque, D.Duquerroy, S.Caston, J.R.Goulas, T.Gomis-Ruth, F.X.

(2015) Proc.Natl.Acad.Sci.USA 112: 8290-8295

  • DOI: 10.1073/pnas.1506538112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa ...

    The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric "snap trap."


    Organizational Affiliation

    Proteolysis Lab, Department of Structural Biology ("María de Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona, Spanish Research Council (CSIC), 08028 Barcelona, Spain;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized lipoprotein YfhM
A
639Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yfhM
Find proteins for P76578 (Escherichia coli (strain K12))
Go to UniProtKB:  P76578
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.720α = 90.00
b = 136.190β = 90.00
c = 172.800γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
SHELXDEphasing
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommunitySpainFP7-PEOPLE-2011-ITN-290246
European CommunitySpainFP7-HEALTH-2012-306029-2
Spanish Ministry for Education, Culture and SportSpainAP2010-3799

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-08
    Type: Database references
  • Version 1.2: 2015-07-15
    Type: Database references
  • Version 1.3: 2019-02-20
    Type: Advisory, Data collection, Derived calculations