1EYR

Structure of a sialic acid activating synthetase, CMP acylneuraminate synthetase in the presence and absence of CDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a sialic acid-activating synthetase, CMP-acylneuraminate synthetase in the presence and absence of CDP.

Mosimann, S.C.Gilbert, M.Dombroswki, D.To, R.Wakarchuk, W.Strynadka, N.C.

(2001) J.Biol.Chem. 276: 8190-8196

  • DOI: 10.1074/jbc.M007235200
  • Primary Citation of Related Structures:  1EZI

  • PubMed Abstract: 
  • The x-ray crystallographic structure of selenomethionyl cytosine-5'-monophosphate-acylneuraminate synthetase (CMP-NeuAc synthetase) from Neisseria meningitidis has been determined at 2.0-A resolution using multiple-wavelength anomalous dispersion pha ...

    The x-ray crystallographic structure of selenomethionyl cytosine-5'-monophosphate-acylneuraminate synthetase (CMP-NeuAc synthetase) from Neisseria meningitidis has been determined at 2.0-A resolution using multiple-wavelength anomalous dispersion phasing, and a second structure, in the presence of the substrate analogue CDP, has been determined at 2.2-A resolution by molecular replacement. This work identifies the active site residues for this class of enzyme for the first time. The detailed interactions between the enzyme and CDP within the mononucleotide-binding pocket are directly observed, and the acylneuraminate-binding pocket has also been identified. A model of acylneuraminate bound to CMP-NeuAc synthetase has been constructed and provides a structural basis for understanding the mechanism of production of "activated" sialic acids. Sialic acids are key saccharide components on the surface of mammalian cells and can be virulence factors in a variety of bacterial species (e.g. Neisseria, Haemophilus, group B streptococci, etc.). As such, the identification of the bacterial CMP-NeuAc synthetase active site can serve as a starting point for rational drug design strategies.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver V6T 1Z3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CMP-N-ACETYLNEURAMINIC ACID SYNTHETASE
A, B
228Neisseria meningitidisGene Names: neuA (siaB, synB)
EC: 2.7.7.43
Find proteins for P0A0Z8 (Neisseria meningitidis)
Go to UniProtKB:  P0A0Z8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDP
Query on CDP

Download SDF File 
Download CCD File 
A, B
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.010α = 90.00
b = 69.890β = 90.00
c = 157.480γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SOLVEphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation