4K3U

Peptidoglycan O-acetylesterase in action, 30 min


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.158 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members.

Williams, A.H.Veyrier, F.J.Bonis, M.Michaud, Y.Raynal, B.Taha, M.K.White, S.W.Haouz, A.Boneca, I.G.

(2014) Acta Crystallogr.,Sect.D 70: 2631-2639

  • DOI: 10.1107/S1399004714016770
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptidoglycan O-acetylesterase (Ape1), which is required for host survival in Neisseria sp., belongs to the diverse SGNH hydrolase superfamily, which includes important viral and bacterial virulence factors. Here, multi-domain crystal structures of A ...

    Peptidoglycan O-acetylesterase (Ape1), which is required for host survival in Neisseria sp., belongs to the diverse SGNH hydrolase superfamily, which includes important viral and bacterial virulence factors. Here, multi-domain crystal structures of Ape1 with an SGNH catalytic domain and a newly identified putative peptidoglycan-detection module are reported. Enzyme catalysis was performed in Ape1 crystals and key catalytic intermediates along the SGNH esterase hydrolysis reaction pathway were visualized, revealing a substrate-induced productive conformation of the catalytic triad, a mechanistic detail that has not previously been observed. This substrate-induced productive conformation of the catalytic triad shifts the established dogma on these enzymes, generating valuable insight into the structure-based design of drugs targeting the SGNH esterase superfamily.


    Organizational Affiliation

    Institut Pasteur, Unité Biologie et génétique de la paroi bactérienne, Dept. Microbiologie, 28 Rue du Dr. Roux, 75015 Paris, France.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Institut Pasteur, Unité Infection Bactériennes Invasives, Dept. Infection et Epidémiologie, 28 Rue du Dr. Roux, 75015 Paris, France.,Institut Pasteur, CNRS-UMR3528, Plateforme de Biophysique, 25 Rue du Dr. Roux, 75724 Paris, France.,Institut Pasteur, CNRS-UMR3528, Plateforme de Cristallographie, 25 Rue du Dr. Roux, 75724 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GDSL-like Lipase/Acylhydrolase family protein
A, B
379N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.158 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.120α = 90.00
b = 80.015β = 90.00
c = 122.113γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing
MxCuBEdata collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references