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 
  • R-Value Observed: 0.190 

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
  • Primary Citation of Related Structures:  
    1Y4H

  • 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 span the active site clefts of their target proteases in the same orientation as substrates ...

    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: 
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cysteine proteaseA, B188Staphylococcus aureusMutation(s): 0 
Gene Names: sspB
EC: 3.4.22
UniProt
Find proteins for P0C1S6 (Staphylococcus aureus)
Explore P0C1S6 
Go to UniProtKB:  P0C1S6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cysteine protease inhibitorC, D109Staphylococcus aureusMutation(s): 0 
Gene Names: sspC
UniProt
Find proteins for Q9EYW6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q9EYW6 
Go to UniProtKB:  Q9EYW6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.948α = 90
b = 77.52β = 108.1
c = 84.891γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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