1W0O

Vibrio cholerae sialidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Sialic Acid Recognition by Vibrio Cholerae Neuraminidase

Moustafa, I.Connaris, H.Taylor, M.Zaitsev, V.Wilsonm, J.C.Kiefel, J.Von-Itzstein, M.Taylor, G.

(2004) J Biol Chem 279: 40819

  • DOI: 10.1074/jbc.M404965200
  • Primary Citation of Related Structures:  
    1W0O, 1W0P

  • PubMed Abstract: 
  • Vibrio cholerae neuraminidase (VCNA) plays a significant role in the pathogenesis of cholera by removing sialic acid from higher order gangliosides to unmask GM1, the receptor for cholera toxin. We previously showed that the structure of VCNA is composed of a central beta-propeller catalytic domain flanked by two lectin-like domains; however the nature of the carbohydrates recognized by these lectin domains has remained unknown ...

    Vibrio cholerae neuraminidase (VCNA) plays a significant role in the pathogenesis of cholera by removing sialic acid from higher order gangliosides to unmask GM1, the receptor for cholera toxin. We previously showed that the structure of VCNA is composed of a central beta-propeller catalytic domain flanked by two lectin-like domains; however the nature of the carbohydrates recognized by these lectin domains has remained unknown. We present here structures of the enzyme in complex with two substrates, alpha-2,3-sialyllactose and alpha-2,6-sialyllactose. Both substrate complexes reveal the alpha-anomer of N-acetylneuraminic acid (Neu5Ac) bound to the N-terminal lectin domain, thereby revealing the role of this domain. The large number of interactions suggest a relatively high binding affinity for sialic acid, which was confirmed by calorimetry, which gave a Kd approximately 30 microm. Saturation transfer difference NMR using a non-hydrolyzable substrate, Neu5,9Ac2-2-S-(alpha-2,6)-GlcNAcbeta1Me, was also used to map the ligand interactions at the VCNA lectin binding site. It is well known that VCNA can hydrolyze both alpha-2,3- and alpha-2,6-linked sialic acid substrates. In this study using alpha-2,3-sialyllactose co-crystallized with VCNA it was revealed that the inhibitor 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en) was bound at the catalytic site. This observation supports the notion that VCNA can produce its own inhibitor and has been further confirmed by 1H NMR analysis. The discovery of the sialic acid binding site in the N-lectin-like domain suggests that this might help target VCNA to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme.


    Organizational Affiliation

    Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIALIDASEA781Vibrio choleraeMutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for P0C6E9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P0C6E9 
Go to UniProtKB:  P0C6E9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
G [auth A]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
DAN (Subject of Investigation/LOI)
Query on DAN

Download Ideal Coordinates CCD File 
B [auth A]2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SIA Binding MOAD:  1W0O Kd: 3.00e+4 (nM) from 1 assay(s)
DAN Binding MOAD:  1W0O Kd: 3.70e+4 (nM) from 1 assay(s)
BindingDB:  1W0O IC50: min: 8600, max: 1.70e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.31α = 90
b = 74.91β = 90
c = 151.615γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary