Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 68.24 kDa 
• Atom Count: 4,989 
• Modelled Residue Count: 582 
• Deposited Residue Count: 600 
• Unique protein chains: 1

 5A8G

Crystal structure of the wild-type Staphylococcus aureus N- acetylneurminic acid lyase in complex with fluoropyruvate

• PDB DOI: 10.2210/pdb5A8G/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-07-15 Released: 2015-11-18 
• Deposition Author(s): Stockwell, J., Daniels, A.D., Windle, C.L., Harman, T., Woodhall, T., Trinh, C.H., Lebel, T., Pearson, A.R., Mulholland, K., Berry, A., Nelson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Evaluation of Fluoropyruvate as Nucleophile in Reactions Catalysed by N-Acetyl Neuraminic Acid Lyase Variants: Scope, Limitations and Stereoselectivity.

Stockwell, J., Daniels, A.D., Windle, C.L., Harman, T.A., Woodhall, T., Lebl, T., Trinh, C.H., Mulholland, K., Pearson, A.R., Berry, A., Nelson, A.

(2016) Org Biomol Chem 14: 105

• PubMed: 26537532 
• DOI: 10.1039/c5ob02037a
• Primary Citation of Related Structures:  
  5A8G


• PubMed Abstract: 
  

The catalysis of reactions involving fluoropyruvate as donor by N-acetyl neuraminic acid lyase (NAL) variants was investigated. Under kinetic control, the wild-type enzyme catalysed the reaction between fluoropyruvate and N-acetyl mannosamine to give a 90 : 10 ratio of the (3R,4R)- and (3S,4R)-configured products; after extended reaction times, equilibration occurred to give a 30 : 70 mixture of these products. The efficiency and stereoselectivity of reactions of a range of substrates catalysed by the E192N, E192N/T167V/S208V and E192N/T167G NAL variants were also studied. Using fluoropyruvate and (2R,3S)- or (2S,3R)-2,3-dihydroxy-4-oxo-N,N-dipropylbutanamide as substrates, it was possible to obtain three of the four possible diastereomeric products; for each product, the ratio of anomeric and pyranose/furanose forms was determined. The crystal structure of S. aureus NAL in complex with fluoropyruvate was determined, assisting rationalisation of the stereochemical outcome of C-C bond formation.

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Organizational Affiliation: 

School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLNEURAMINATE LYASE	A, B	300	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: nanA, SAOUHSC_00295 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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPF	A, B	L-PEPTIDE LINKING	C9 H15 F N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.587	α = 90
b = 150.396	β = 90
c = 140.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Stockwell, J., Daniels, A.D., Windle, C.L., Harman, T., Woodhall, T., Trinh, C.H., Lebel, T., Pearson, A.R., Mulholland, K., Berry, A., Nelson, A.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references