5KZD | pdb_00005kzd

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 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

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 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.
Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
Protein Science and Engineering, Callaghan Innovation, University of Canterbury, Christchurch, New Zealand.
Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Sweden.
Department of Structural Biology, School of Medicine, Stanford University, CA, USA.
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.

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 
• Modeled 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

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