A comparison of staphostatin B with standard mechanism serine protease inhibitors.
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.
Filipek
Renata
R
International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.
Potempa
Jan
J
Bochtler
Matthias
M
D001426:Bacterial Proteins / Q000737:chemistry* / Q000494:pharmacology*; D001665:Binding Sites; D001667:Binding, Competitive; D002352:Carrier Proteins / Q000737:chemistry* / Q000494:pharmacology*; D002384:Catalysis; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000494:pharmacology; D047908:Intracellular Signaling Peptides and Proteins; D007477:Ions; D008958:Models, Molecular; D008962:Models, Theoretical; D016297:Mutagenesis, Site-Directed; D010100:Oxygen / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012697:Serine Endopeptidases / Q000737:chemistry; D015842:Serine Proteinase Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D013211:Staphylococcus aureus / Q000378:metabolism; D013455:Sulfur / Q000737:chemistry; D014867:Water / Q000737:chemistry
D001426:Bacterial Proteins; D002352:Carrier Proteins; D004791:Enzyme Inhibitors; D047908:Intracellular Signaling Peptides and Proteins; D007477:Ions; D010455:Peptides; D015842:Serine Proteinase Inhibitors; C479136:staphostatin B protein, Staphylococcus aureus; D014867:Water; D013455:Sulfur; D012697:Serine Endopeptidases; D003545:Cysteine; D010100:Oxygen