2VID

Serine protease SplB from Staphylococcus aureus at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Enzymatic Activity of the Staphylococcus Aureus Splb Serine Protease is Induced by Substrates Containing the Sequence Trp-Glu-Leu-Gln.

Dubin, G.Stec-Niemczyk, J.Kisielewska, M.Pustelny, K.Popowicz, G.M.Bista, M.Kantyka, T.Boulware, K.T.Stennicke, H.R.Czarna, A.Phopaisarn, M.Daugherty, P.S.Thogersen, I.B.Enghild, J.J.Thornberry, N.Dubin, A.Potempa, J.

(2008) J Mol Biol 379: 343

  • DOI: 10.1016/j.jmb.2008.03.059
  • Primary Citation of Related Structures:  
    2VID

  • PubMed Abstract: 
  • Proteases are of significant importance for the virulence of Staphylococcus aureus. Nevertheless, their subset, the serine protease-like proteins, remains poorly characterized. Here presented is an investigation of SplB protease catalytic activity re ...

    Proteases are of significant importance for the virulence of Staphylococcus aureus. Nevertheless, their subset, the serine protease-like proteins, remains poorly characterized. Here presented is an investigation of SplB protease catalytic activity revealing that the enzyme possesses exquisite specificity and only cleaves efficiently after the sequence Trp-Glu-Leu-Gln. To understand the molecular basis for such selectivity, we solved the three-dimensional structure of SplB to 1.8 A. Modeling of substrate binding to the protease demonstrated that selectivity relies in part on a canonical specificity pockets-based mechanism. Significantly, the conformation of residues that ordinarily form the oxyanion hole, an essential structural element of the catalytic machinery of serine proteases, is not canonical in the SplB structure. We postulate that within SplB, the oxyanion hole is only formed upon docking of a substrate containing the consensus sequence motif. It is suggested that this unusual activation mechanism is used in parallel with classical determinants to further limit enzyme specificity. Finally, to guide future development, we attempt to point at likely physiological substrates and thus the role of SplB in staphylococcal physiology.


    Related Citations: 
    • Functional and Structural Characterization of Spl Proteases from Staphylococcus Aureus
      Popowicz, G.M., Dubin, G., Stec-Niemczyk, J., Czarny, A., Dubin, A., Potempa, J., Holak, T.A.
      (2006) J Mol Biol 358: 270

    Organizational Affiliation

    Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland. gdubin@mol.uj.edu.pl



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PROTEASE SPLBAB204Staphylococcus aureusMutation(s): 0 
EC: 3.4.21
Find proteins for Q2FXC3 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXC3 
Go to UniProtKB:  Q2FXC3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.475α = 90
b = 117.475β = 90
c = 73.293γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation