2JKB

Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac

• PDB DOI: https://doi.org/10.2210/pdb2JKB/pdb

• Classification: LYASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-08-26 Released: 2008-09-16 
• Deposition Author(s): Gut, H., King, S.J., Walsh, M.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.188 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Starting Model: in silico

Literature

Structural and Functional Studies of Streptococcus Pneumoniae Neuraminidase B: An Intramolecular Trans-Sialidase.

Gut, H., King, S.J., Walsh, M.A.

(2008) FEBS Lett 582: 3348

• PubMed: 18775704 
• DOI: https://doi.org/10.1016/j.febslet.2008.08.026
• Primary Citation of Related Structures:  
  2JKB


• PubMed Abstract: 
  

  The human pathogen Streptococcus pneumoniae expresses neuraminidase proteins that cleave sialic acids from complex carbohydrates. The pneumococcus genome encodes up to three neuraminidase proteins that have been shown to be important virulence factors. Here, we report the first structure of a neuraminidase from S. pneumoniae: the crystal structure of NanB in complex with its reaction product 2,7-anhydro-Neu5Ac. Our structural data, together with biochemical analysis, establish NanB as an intramolecular trans-sialidase with strict specificity towards alpha2-3 linked sialic acid substrates. In addition, we show that NanB differs in its substrate specificity from the other pneumococcal neuraminidase NanA.

---

Organizational Affiliation: 

MRC France, BM14 c/o ESRF, 6 rue Jules Horowitz, BP220, 38043 Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 77.4 kDa 
• Atom Count: 6,507 
• Modelled Residue Count: 661 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIALIDASE B	A	686	Streptococcus pneumoniae TIGR4	Mutation(s): 0  EC: 4.2.2.15 (PDB Primary Data), 3.2.1.18 (UniProt)
UniProt
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q54727  Go to UniProtKB:  Q54727

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SKD	B [auth A]	2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID C11 H17 N O8 NCMJSVDTRDLWJE-YRMXFSIDSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.188 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.719	α = 90
b = 82.746	β = 90
c = 118.079	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Gut, H., King, S.J., Walsh, M.A.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Other, Refinement description