4YZ5

Crystal Structure of Streptococcus pneumoniae NanC, in complex with 3-Sialyllactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR.

Owen, C.D.Lukacik, P.Potter, J.A.Sleator, O.Taylor, G.L.Walsh, M.A.

(2015) J.Biol.Chem. 290: 27736-27748

  • DOI: 10.1074/jbc.M115.673632
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Streptococcus pneumoniae is an important human pathogen that causes a range of disease states. Sialidases are important bacterial virulence factors. There are three pneumococcal sialidases: NanA, NanB, and NanC. NanC is an unusual sialidase in that i ...

    Streptococcus pneumoniae is an important human pathogen that causes a range of disease states. Sialidases are important bacterial virulence factors. There are three pneumococcal sialidases: NanA, NanB, and NanC. NanC is an unusual sialidase in that its primary reaction product is 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en, also known as DANA), a nonspecific hydrolytic sialidase inhibitor. The production of Neu5Ac2en from α2-3-linked sialosides by the catalytic domain is confirmed within a crystal structure. A covalent complex with 3-fluoro-β-N-acetylneuraminic acid is also presented, suggesting a common mechanism with other sialidases up to the final step of product formation. A conformation change in an active site hydrophobic loop on ligand binding constricts the entrance to the active site. In addition, the distance between the catalytic acid/base (Asp-315) and the ligand anomeric carbon is unusually short. These features facilitate a novel sialidase reaction in which the final step of product formation is direct abstraction of the C3 proton by the active site aspartic acid, forming Neu5Ac2en. NanC also possesses a carbohydrate-binding module, which is shown to bind α2-3- and α2-6-linked sialosides, as well as N-acetylneuraminic acid, which is captured in the crystal structure following hydration of Neu5Ac2en by NanC. Overall, the pneumococcal sialidases show remarkable mechanistic diversity while maintaining a common structural scaffold.


    Organizational Affiliation

    Diamond Light Source and the Medical Research Council France, c/o European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France martin.walsh@diamond.ac.uk.,Diamond Light Source and Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom, and.,From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom, glt2@st-andrews.ac.uk.,From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom.,the Medical Research Council France, c/o European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative neuraminidase
A, B
677Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
EC: 3.2.1.18
Find proteins for A0A0H2UQE4 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2UQE4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DAN
Query on DAN

Download SDF File 
Download CCD File 
A, B
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
 Ligand Interaction
SLT
Query on SLT

Download SDF File 
Download CCD File 
A, B
5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE
LACTOSE SIALIC ACID; ALPHA(2,3) SIALYL LACTOSE
C23 H39 N O19
CILYIEBUXJIHCO-LPTWSRJFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SLTKd: 1480000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.470α = 90.00
b = 136.570β = 90.00
c = 150.070γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PDB_EXTRACTdata extraction
xia2data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence