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 
  • R-Value Observed: 0.165 

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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: https://doi.org/10.1021/bi9012758
  • Primary Citation of Related Structures:  
    2WQP

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC349Neisseria meningitidis serogroup BMutation(s): 1 
UniProt
Find proteins for Q7DDU0 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q7DDU0 
Go to UniProtKB:  Q7DDU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DDU0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WQP
Query on WQP

Download Ideal Coordinates CCD File 
B [auth A]5-(ACETYLAMINO)-3,5-DIDEOXY-2-O-PHOSPHONO-D-ERYTHRO-L-MANNO-NONONIC ACID
C11 H22 N O12 P
SQZISPQQTAMDAM-IHICSVBISA-N
LMR
Query on LMR

Download Ideal Coordinates CCD File 
I [auth A](2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
WQP PDBBind:  2WQP Ki: 3100 (nM) from 1 assay(s)
Binding MOAD:  2WQP Ki: 3100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.619α = 90
b = 75.744β = 90
c = 77.361γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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