2WQP

Crystal structure of sialic acid synthase NeuB-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Inhibition of Neisseria Meningitidis Sialic Acid Synthase by a Tetrahedral Intermediate Analog.

Liu, F.Lee, H.J.Strynadka, N.C.J.Tanner, M.E.

(2009) Biochemistry 48: 9194

  • DOI: 10.1021/bi9012758

  • PubMed Abstract: 
  • The Neisseria meningitidis sialic acid synthase (NeuB) catalyzes the metal-dependent condensation of N-acetylmannosamine (ManNAc) and phosphoenolpyruvate (PEP) to generate N-acetylneuraminic acid (NeuAc or sialic acid). N. meningitidis is a causative ...

    The Neisseria meningitidis sialic acid synthase (NeuB) catalyzes the metal-dependent condensation of N-acetylmannosamine (ManNAc) and phosphoenolpyruvate (PEP) to generate N-acetylneuraminic acid (NeuAc or sialic acid). N. meningitidis is a causative agent of meningitis and produces a capsular polysaccharide comprised of polysialic acid. This allows it to evade the immune system of the host by an act of molecular mimicry. This work describes the synthesis and characterization of the first potent inhibitor of sialic acid synthase. The inhibitor is a stable deoxy analogue of the tetrahedral intermediate presumed to form in the NeuB reaction and was synthesized as a mixture of stereoisomers at the key tetrahedral center. Inhibition studies demonstrate that one stereoisomer binds more tightly than the other and that the more potent isomer binds with micromolar affinity. An X-ray crystallographic analysis of the NeuB.inhibitor.Mn(2+) complex solved to a resolution of 1.75 A shows that the more tightly bound stereoisomer bears a (2R)-configuration. This suggests that the tetrahedral intermediate formed in the NeuB reaction also bears a (2R)-configuration. This analysis is consistent with a mechanism whereby the active site metal plays at least two roles during catalysis. First, it serves as an electrostatic catalyst and activates the aldehyde of ManNAc for attack by the alkene of PEP. Second, it serves as a source of nucleophilic water and delivers it to the si face of the oxocarbenium intermediate to generate a tetrahedral intermediate with a (2R)-configuration.


    Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC
A
349Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 1 
Gene Names: siaC
Find proteins for Q7DDU0 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q7DDU0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
LMR
Query on LMR

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Download CCD File 
A
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
WQP
Query on WQP

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Download CCD File 
A
5-(ACETYLAMINO)-3,5-DIDEOXY-2-O-PHOSPHONO-D-ERYTHRO-L-MANNO-NONONIC ACID
C11 H22 N O12 P
SQZISPQQTAMDAM-IHICSVBISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WQPKi: 3100 nM BINDINGMOAD
WQPKi: 3100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.619α = 90.00
b = 75.744β = 90.00
c = 77.361γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-10-12
    Type: Database references