6PPW

Crystal structure of NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis, in complex with magnesium and malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB.

Popovic, V.Morrison, E.Rosanally, A.Z.Balachandran, N.Senson, A.W.Szabla, R.Junop, M.S.Berti, P.J.

(2019) Biochemistry 58: 4236-4245

  • DOI: 10.1021/acs.biochem.9b00654
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NeuB is a bacterial sialic acid synthase used by neuroinvasive bacteria to synthesize <i>N </i>-acetylneuraminate (NeuNAc), helping them to evade the host immune system. NeuNAc oxime is a potent slow-binding NeuB inhibitor. It dissociated too slowly ...

    NeuB is a bacterial sialic acid synthase used by neuroinvasive bacteria to synthesize N -acetylneuraminate (NeuNAc), helping them to evade the host immune system. NeuNAc oxime is a potent slow-binding NeuB inhibitor. It dissociated too slowly to be detected experimentally, with initial estimates of its residence time in the active site being >47 days. This is longer than the lifetime of a typical bacterial cell, meaning that inhibition is effectively irreversible. Inhibition data fitted well to a model that included a pre-equilibration step with a K i of 36 μM, followed by effectively irreversible conversion to an E*·I complex, with a k 2 of 5.6 × 10 -5 s -1 . Thus, the inhibitor can subvert ligand release and achieve extraordinary residence times in spite of a relatively modest initial dissociation constant. The crystal structure showed the oxime functional group occupying the phosphate-binding site normally occupied by the substrate PEP and the tetrahedral intermediate. There was an ≈10% residual rate at high inhibitor concentrations regardless of how long NeuB and NeuNAc oxime were preincubated together. However, complete inhibition was achieved by incubating NeuNAc oxime with the actively catalyzing enzyme. This requirement for the enzyme to be actively turning over for the inhibitor to bind to the second subunit demonstrated an important role for intersubunit communication in the inhibitory mechanism.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology Lab , Western University , London , ON N6A 5C1 , Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylneuraminate synthase
A
349Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: synC
EC: 2.5.1.56
Find proteins for H2VFG5 (Neisseria meningitidis serogroup B)
Go to UniProtKB:  H2VFG5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLT
Query on MLT

Download SDF File 
Download CCD File 
A
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.793α = 90.00
b = 76.030β = 90.00
c = 77.370γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-64422
Canadian Institutes of Health Research (CIHR)CanadaMOP-89903

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Advisory, Data collection
  • Version 1.2: 2019-10-23
    Type: Data collection, Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence