4K1T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.2 of the entry. See complete history


Literature

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: 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 ...

    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

    the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30 387 Krakow, Poland, the Malopolska Centre of Biotechnology, 30 387 Krakow, Poland grzegorz.dubin@uj.edu.pl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease SplBA, B, C206Staphylococcus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], L [auth A], N [auth B], Q [auth B], U [auth C], X [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , K [auth A] , M [auth B] , O [auth B] , P [auth B] , T [auth C] , 
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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A], R [auth B], S [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
Cootmodel building
REFMACrefinement
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