5KZD

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


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 

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Ligand Structure Quality Assessment 


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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

  • DOI: 10.1002/1873-3468.12462
  • Primary Citation of Related Structures:  
    5KZE, 5KZD

  • 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylneuraminate lyaseA, B, C, D293Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
Gene Names: nanASAUSA300_0315
EC: 4.1.3.3
UniProt
Find proteins for Q2G160 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G160 
Go to UniProtKB:  Q2G160
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RCJ (Subject of Investigation/LOI)
Query on RCJ

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 81.477α = 90
b = 109.444β = 90
c = 130.752γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release