1Y4H

Wild type staphopain-staphostatin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A comparison of staphostatin B with standard mechanism serine protease inhibitors.

Filipek, R.Potempa, J.Bochtler, M.

(2005) J.Biol.Chem. 280: 14669-14674

  • DOI: 10.1074/jbc.M411792200

  • PubMed Abstract: 
  • Staphostatins are the endogenous, highly specific inhibitors of staphopains, the major secreted cysteine proteases from Staphylococcus aureus. We have previously shown that staphostatins A and B are competitive, active site-directed inhibitors that s ...

    Staphostatins are the endogenous, highly specific inhibitors of staphopains, the major secreted cysteine proteases from Staphylococcus aureus. We have previously shown that staphostatins A and B are competitive, active site-directed inhibitors that span the active site clefts of their target proteases in the same orientation as substrates. We now report the crystal structure of staphostatin B in complex with wild-type staphopain B at 1.9 A resolution. In the complex structure, the catalytic residues are found in exactly the positions that would be expected for uncomplexed papain-type proteases. There is robust, continuous density for the staphostatin B binding loop and no indication for cleavage of the peptide bond that comes closest to the active site cysteine of staphopain B. The carbonyl carbon atom C of this peptide bond is 4.1 A away from the active site cysteine sulfur Sgamma atom. The carbonyl oxygen atom O of this peptide bond points away from the putative oxyanion hole and lies almost on a line from the Sgamma atom to the C atom. The arrangement is strikingly similar to the "ionmolecule" arrangement for the complex of papain-type enzymes with their substrates but differs significantly from the arrangement conventionally assumed for the Michaelis complex of papain-type enzymes with their substrates and also from the arrangement that is crystallographically observed for complexes of standard mechanism inhibitors and their target serine proteases.


    Related Citations: 
    • Staphostatins: an expanding new group of proteinase inhibitors with a unique specificity for the regulation of staphopains, Staphylococcus spp. cysteine proteinases.
      Rzychon, M.,Sabat, A.,Kosowska, K.,Potempa, J.,Dubin, A.
      (2003) Mol.Microbiol. 49: 1051
    • Staphostatins resemble lipocalins, not cystatins in fold.
      Rzychon, M.,Filipek, R.,Sabat, A.,Kosowska, K.,Dubin, A.,Potempa, J.,Bochtler, M.
      (2003) Protein Sci. 12: 2252
    • Prostaphopain B structure: a comparison of proregion-mediated and staphostatin-mediated protease inhibition.
      Filipek, R.,Szczepanowski, R.,Sabat, A.,Potempa, J.,Bochtler, M.
      (2004) Biochemistry 43: 14306
    • The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease.
      Filipek, R.,Rzychon, M.,Oleksy, A.,Gruca, M.,Dubin, A.,Potempa, J.,Bochtler, M.
      (2003) J.Biol.Chem. 278: 40959


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cysteine protease
A, B
188Staphylococcus aureusMutation(s): 0 
Gene Names: sspB
EC: 3.4.22.-
Find proteins for P0C1S6 (Staphylococcus aureus)
Go to UniProtKB:  P0C1S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cysteine protease inhibitor
C, D
109Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: sspC
Find proteins for Q9EYW6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q9EYW6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.948α = 90.00
b = 77.520β = 108.10
c = 84.891γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references