5KZD

N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus with bound sialic acid alditol

• PDB DOI: https://doi.org/10.2210/pdb5KZD/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus USA300
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-25 Released: 2017-01-11 
• Deposition Author(s): North, R.A., Watson, A.J.A., Pearce, F.G., Muscroft-Taylor, A.C., Friemann, R., Fairbanks, A.J., Dobson, R.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.261 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus.

North, R.A., Watson, A.J., Pearce, F.G., Muscroft-Taylor, A.C., Friemann, R., Fairbanks, A.J., Dobson, R.C.

(2016) FEBS Lett 590: 4414-4428

• PubMed: 27943302 
• DOI: https://doi.org/10.1002/1873-3468.12462
• Primary Citation of Related Structures:  
  5KZD, 5KZE


• PubMed Abstract: 
  

  N-Acetylneuraminate lyase is the first committed enzyme in the degradation of sialic acid by bacterial pathogens. In this study, we analyzed the kinetic parameters of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus (MRSA). We determined that the enzyme has a relatively high K _M of 3.2 mm, suggesting that flux through the catabolic pathway is likely to be controlled by this enzyme. Our data indicate that sialic acid alditol, a known inhibitor of N-acetylneuraminate lyase enzymes, is a stronger inhibitor of MRSA N-acetylneuraminate lyase than of Clostridium perfringens N-acetylneuraminate lyase. Our analysis of the crystal structure of ligand-free and 2R-sialic acid alditol-bound MRSA N-acetylneuraminate lyase suggests that subtle dynamic differences in solution and/or altered binding interactions within the active site may account for species-specific inhibition.

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Organizational Affiliation: 

Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 133.55 kDa 
• Atom Count: 9,341 
• Modelled Residue Count: 1,136 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D	293	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0  Gene Names: nanA, SAUSA300_0315 EC: 4.1.3.3
UniProt
Find proteins for Q2G160 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G160  Go to UniProtKB:  Q2G160

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RCJ	E [auth A], F [auth B], G [auth C], H [auth D]	(2~{S},4~{S},5~{R},6~{R},7~{S},8~{R})-5-acetamido-2,4,6,7,8,9-hexakis(oxidanyl)nonanoic acid C11 H21 N O9 REORMAHRVILHOU-HQBQHRAMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RCJ	Binding MOAD:  5KZD	Ki: 3.90e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.261 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.477	α = 90
b = 109.444	β = 90
c = 130.752	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): North, R.A., Watson, A.J.A., Pearce, F.G., Muscroft-Taylor, A.C., Friemann, R., Fairbanks, A.J., Dobson, R.C.J.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references