6PPY

Crystal structure of NeuNAc oxime complexed with NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    6PPW, 6PPX, 6PPY, 6PPZ

  • PubMed Abstract: 

    • 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylneuraminate synthaseA349Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: synC
EC: 2.5.1.56
UniProt
Find proteins for H2VFG5 (Neisseria meningitidis serogroup B)
Explore H2VFG5 
Go to UniProtKB:  H2VFG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2VFG5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OVY (Subject of Investigation/LOI)
Query on OVY
Download Ideal Coordinates CCD File 
B [auth A](2E,4S,5R,6R,7S,8R)-5-(acetylamino)-4,6,7,8,9-pentahydroxy-2-(hydroxyimino)nonanoic acid (non-preferred name)
C11 H20 N2 O9
ROZSOFSDDJZICT-HMLDMLNFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.11α = 90
b = 76.04β = 90
c = 77.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

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  (Full details and data files)

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