4AMA

Crystal Structure of N-acetylneuraminic acid lyase from Staphylococcus aureus with the chemical modification thia-lysine at position 165 in complex with pyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with gamma-thialysine by using a chemical mutagenesis strategy.

Timms, N.Windle, C.L.Polyakova, A.Ault, J.R.Trinh, C.H.Pearson, A.R.Nelson, A.Berry, A.

(2013) Chembiochem 14: 474-481

  • DOI: 10.1002/cbic.201200714
  • Primary Citation of Related Structures:  
    4AH7, 4AHO, 4AHP, 4AHQ, 4AMA

  • PubMed Abstract: 
  • Chemical modification has been used to introduce the unnatural amino acid γ-thialysine in place of the catalytically important Lys165 in the enzyme N-acetylneuraminic acid lyase (NAL). The Staphylococcus aureus nanA gene, encoding NAL, was cloned and expressed in E ...

    Chemical modification has been used to introduce the unnatural amino acid γ-thialysine in place of the catalytically important Lys165 in the enzyme N-acetylneuraminic acid lyase (NAL). The Staphylococcus aureus nanA gene, encoding NAL, was cloned and expressed in E. coli. The protein, purified in high yield, has all the properties expected of a class I NAL. The S. aureus NAL which contains no natural cysteine residues was subjected to site-directed mutagenesis to introduce a cysteine in place of Lys165 in the enzyme active site. Subsequently chemical mutagenesis completely converted the cysteine into γ-thialysine through dehydroalanine (Dha) as demonstrated by ESI-MS. Initial kinetic characterisation showed that the protein containing γ-thialysine regained 17 % of the wild-type activity. To understand the reason for this lower activity, we solved X-ray crystal structures of the wild-type S. aureus NAL, both in the absence of, and in complex with, pyruvate. We also report the structures of the K165C variant, and the K165-γ-thialysine enzyme in the presence, or absence, of pyruvate. These structures reveal that γ-thialysine in NAL is an excellent structural mimic of lysine. Measurement of the pH-activity profile of the thialysine modified enzyme revealed that its pH optimum is shifted from 7.4 to 6.8. At its optimum pH, the thialysine-containing enzyme showed almost 30 % of the activity of the wild-type enzyme at its pH optimum. The lowered activity and altered pH profile of the unnatural amino acid-containing enzyme can be rationalised by imbalances of the ionisation states of residues within the active site when the pK(a) of the residue at position 165 is perturbed by replacement with γ-thialysine. The results reveal the utility of chemical mutagenesis for the modification of enzyme active sites and the exquisite sensitivity of catalysis to the local structural and electrostatic environment in NAL.


    Related Citations: 
    • Structural Insights Into the Recovery of Aldolase Activity in N-Acetylneuraminic Acid Lyase by Replacement of the Catalytically Active Lysine with Gamma-Thialysine by Using a Chemical Mutagenesis Strategy.
      Timms, N., Windle, C.L., Polyakova, A., Ault, J.R., Trinh, C.H., Pearson, A.R., Nelson, A., Berry, A.
      (2013) Chembiochem 14: 474

    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang Building, Leeds, LS2 9JT, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-ACETYLNEURAMINATE LYASEA, B, C, D298Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: nanASAOUHSC_00295
EC: 4.1.3.3
UniProt
Find proteins for Q2G160 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G160 
Go to UniProtKB:  Q2G160
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G160
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPY
Query on KPY
A, B, C, D L-PEPTIDE LINKINGC8 H14 N2 O4 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.935α = 90
b = 110.278β = 90
c = 132.241γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references, Structure summary
  • Version 2.0: 2019-05-15
    Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence
  • Version 2.1: 2019-07-10
    Changes: Data collection