Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.15 kDa 
• Atom Count: 2933 
• Modelled Residue Count: 326 
• Deposited Residue Count: 326 
• Unique protein chains: 1

2YK5

Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP.

• DOI: 10.2210/pdb2YK5/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria meningitidis serogroup B
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-05-25 Released: 2011-08-31 
• Deposition Author(s): Lin, L.Y.C., Rakic, B., Chiu, C.P.C., Lameignere, E., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.223 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Structure and Mechanism of the Lipooligosaccharide Sialyltransferase from Neisseria Meningitidis

Lin, L.Y.C., Rakic, B., Chiu, C.P.C., Lameignere, E., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

(2011) J Biol Chem 286: 37237

• PubMed: 21880735 
• DOI: 10.1074/jbc.M111.249920
• Primary Citation of Related Structures:  
  2YK4, 2YK5, 2YK6, 2YK7


• PubMed Abstract: 
  

The first x-ray crystallographic structure of a CAZY family-52 glycosyltransferase, that of the membrane associated α2,3/α2,6 lipooligosaccharide sialyltransferase from Neisseria meningitidis serotype L1 (NST), has been solved to 1.95 Å resolution. The structure of NST adopts a GT-B-fold common with other glycosyltransferase (GT) families but exhibits a novel domain swap of the N-terminal 130 residues to create a functional homodimeric form not observed in any other class to date. The domain swap is mediated at the structural level by a loop-helix-loop extension between residues Leu-108 and Met-130 (we term the swapping module) and a unique lipid-binding domain. NST catalyzes the creation of α2,3- or 2,6-linked oligosaccharide products from a CMP-sialic acid (Neu5Ac) donor and galactosyl-containing acceptor sugars. Our structures of NST bound to the non-hydrolyzable substrate analog CMP-3F((axial))-Neu5Ac show that the swapping module from one monomer of NST mediates the binding of the donor sugar in a composite active site formed at the dimeric interface. Kinetic analysis of designed point mutations observed in the CMP-3F((axial))-Neu5Ac binding site suggests potential roles of a requisite general base (Asp-258) and general acid (His-280) in the NST catalytic mechanism. A long hydrophobic tunnel adjacent to the dimer interface in each of the two monomers contains electron density for two extended linear molecules that likely belong to either the two fatty acyl chains of a diglyceride lipid or the two polyethylene glycol groups of the detergent Triton X-100. In this work, Triton X-100 maintains the activity and increases the solubility of NST during purification and is critical to the formation of ordered crystals. Together, the mechanistic implications of the NST structure provide insight into lipooligosaccharide sialylation with respect to the association of substrates and the essential membrane-anchored nature of NST on the bacterial surface.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Centre for Blood Research University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE	A	326	Neisseria meningitidis serogroup B	Mutation(s): 5  EC: 2.4.99 (PDB Primary Data), 2.4.99.6 (UniProt)
UniProt
Find proteins for P72097 (Neisseria meningitidis serogroup B (strain MC58)) Explore P72097  Go to UniProtKB:  P72097

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C (Subject of Investigation/LOI)	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N
1PE	D [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.223 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.747	α = 90
b = 124.137	β = 90
c = 41.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-25 
• Released Date: 2011-08-31 
Deposition Author(s): Lin, L.Y.C., Rakic, B., Chiu, C.P.C., Lameignere, E., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references
• Version 1.2: 2017-07-05
  Changes: Refinement description
• Version 1.3: 2019-09-25
  Changes: Data collection, Derived calculations, Experimental preparation, Other