2RKS

Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values.

Harms, M.J.Schlessman, J.L.Chimenti, M.S.Sue, G.R.Damjanovic, A.Garcia-Moreno, B.

(2008) Protein Sci 17: 833-845

  • DOI: https://doi.org/10.1110/ps.073397708
  • Primary Citation of Related Structures:  
    2RKS

  • PubMed Abstract: 

    Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pK(a) values shifted by up to 5 pK(a) units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pK(a). The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is approximately 7 A from solvent and ion paired with Glu-122. This suggests that the pK(a) value of Lys-38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pK(a) of Lys-38 was also normal when Glu-122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pK(a) of Lys-38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pK(a) value of Lys-38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native-like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys-38 and Glu-122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys-38. This illustrates both the important roles of local flexibility and water penetration as determinants of pK(a) values of ionizable groups buried near the protein-water interface, and the challenges faced by structure-based pK(a) calculations in reproducing these effects.


  • Organizational Affiliation

    Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermonuclease149Staphylococcus aureusMutation(s): 4 
Gene Names: nuc
EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus)
Explore P00644 
Go to UniProtKB:  P00644
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00644
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.206 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.684α = 90
b = 48.684β = 90
c = 62.521γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2024-02-21
    Changes: Data collection
  • Version 1.5: 2024-04-03
    Changes: Refinement description