2X63 | pdb_00002x63

Crystal structure of the sialyltransferase CST-II N51A in complex with CMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.230 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2X63

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Structural and Kinetic Analysis of Substrate Binding to the Sialyltransferase Cst-II from Campylobacter Jejuni.

Lee, H.J.Lairson, L.L.Rich, J.R.Lameignere, E.Wakarchuk, W.W.Withers, S.G.Strynadka, N.C.J.

(2011) J Biological Chem 286: 35922

  • DOI: https://doi.org/10.1074/jbc.M111.261172
  • Primary Citation Related Structures: 
    2X61, 2X62, 2X63

  • PubMed Abstract: 

    Sialic acids play important roles in various biological processes and typically terminate the oligosaccharide chains on the cell surfaces of a wide range of organisms, including mammals and bacteria. Their attachment is catalyzed by a set of sialyltransferases with defined specificities both for their acceptor sugars and the position of attachment. However, little is known of how this specificity is encoded. The structure of the bifunctional sialyltransferase Cst-II of the human pathogen Campylobacter jejuni in complex with CMP and the terminal trisaccharide of its natural acceptor (Neu5Ac-α-2,3-Gal-β-1,3-GalNAc) has been solved at 1.95 Å resolution, and its kinetic mechanism was shown to be iso-ordered Bi Bi, consistent with its dual acceptor substrate specificity. The trisaccharide acceptor is seen to bind to the active site of Cst-II through interactions primarily mediated by Asn-51, Tyr-81, and Arg-129. Kinetic and structural analyses of mutants modified at these positions indicate that these residues are critical for acceptor binding and catalysis, thereby providing significant new insight into the kinetic and catalytic mechanism, and acceptor specificity of this pathogen-encoded bifunctional GT-42 sialyltransferase.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3.

Macromolecule Content 

  • Total Structure Weight: 30.73 kDa 
  • Atom Count: 2,357 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 258 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALPHA-2,3-/2,8-SIALYLTRANSFERASE258Campylobacter jejuniMutation(s): 3 
EC: 2.4.99
UniProt
Find proteins for Q9LAK3 (Campylobacter jejuni)
Explore Q9LAK3 
Go to UniProtKB:  Q9LAK3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LAK3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.230 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.19α = 90
b = 116.19β = 90
c = 46.951γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references, Version format compliance
  • Version 1.2: 2011-10-19
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.0: 2025-12-17
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary