Gly-Ser-SplB protease from Staphylococcus aureus at 1.60 A resolution

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Staphylococcal SplB Serine Protease Utilizes a Novel Molecular Mechanism of Activation.

Pustelny, K.Zdzalik, M.Stach, N.Stec-Niemczyk, J.Cichon, P.Czarna, A.Popowicz, G.Mak, P.Drag, M.Salvesen, G.S.Wladyka, B.Potempa, J.Dubin, A.Dubin, G.

(2014) J Biol Chem 289: 15544-15553

  • DOI: https://doi.org/10.1074/jbc.M113.507616
  • Primary Citation of Related Structures:  
    4K1S, 4K1T

  • PubMed Abstract: 

    Staphylococcal SplB protease belongs to the chymotrypsin family. Chymotrypsin zymogen is activated by proteolytic processing at the N terminus, resulting in significant structural rearrangement at the active site. Here, we demonstrate that the molecular mechanism of SplB protease activation differs significantly and we characterize the novel mechanism in detail. Using peptide and protein substrates we show that the native signal peptide, or any N-terminal extension, has an inhibitory effect on SplB. Only precise N-terminal processing releases the full proteolytic activity of the wild type analogously to chymotrypsin. However, comparison of the crystal structures of mature SplB and a zymogen mimic show no rearrangement at the active site whatsoever. Instead, only the formation of a unique hydrogen bond network, distant form the active site, by the new N-terminal glutamic acid of mature SplB is observed. The importance of this network and influence of particular hydrogen bond interactions at the N terminus on the catalytic process is demonstrated by evaluating the kinetics of a series of mutants. The results allow us to propose a consistent model where changes in the overall protein dynamics rather than structural rearrangement of the active site are involved in the activation process.

  • Organizational Affiliation

    From the Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the NMR Group, Max-Planck Institute for Biochemistry, 82 152 Martinsried, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease SplB
A, B, C
206Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: splBSAOUHSC_01941
EC: 3.4.21
Find proteins for Q2FXC3 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXC3 
Go to UniProtKB:  Q2FXC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXC3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth A]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
L [auth A],
N [auth B],
Q [auth B],
U [auth C],
X [auth C]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
K [auth A]
M [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth A],
M [auth B],
O [auth B],
P [auth B],
T [auth C],
V [auth C],
W [auth C]
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
R [auth B],
S [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.74α = 90
b = 77.76β = 131.81
c = 95.79γ = 90
Software Package:
Software NamePurpose
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description