2VID

Serine protease SplB from Staphylococcus aureus at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE SPLB
A, B
204Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: splB
EC: 3.4.21.-
Find proteins for Q2FXC3 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXC3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 117.475α = 90.00
b = 117.475β = 90.00
c = 73.293γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance