4INK

Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution

Summary for 4INK

• Entry DOI: 10.2210/pdb4ink/pdb
• Related: 4INL
• Descriptor: Serine protease SplD (2 entities in total)
• Functional Keywords: chymotrypsin-like protease, serine endopeptidase, extracellular staphylococcal proteases, hydrolase
• Biological source: Staphylococcus aureus subsp. aureus
• Cellular location: Secreted : Q2FXC5
• Total number of polymer chains: 1
• Total formula weight: 22181.92

Authors

Zdzalik, M.,Kalinska, M.,Cichon, P.,Wysocka, M.,Stec-Niemczyk, J.,Stennicke, H.R.,Jabaiah, A.,Markiewicz, M.,Wladyka, B.,Daugherty, P.S.,Lesner, A.,Rolka, K.,Dubin, A.,Potempa, J.,Dubin, G. (deposition date: 2013-01-04, release date: 2013-10-30, Last modification date: 2023-09-20)

Primary citation

Zdzalik, M.,Kalinska, M.,Wysocka, M.,Stec-Niemczyk, J.,Cichon, P.,Stach, N.,Gruba, N.,Stennicke, H.R.,Jabaiah, A.,Markiewicz, M.,Kedracka-Krok, S.,Wladyka, B.,Daugherty, P.S.,Lesner, A.,Rolka, K.,Dubin, A.,Potempa, J.,Dubin, G.
Biochemical and Structural Characterization of SplD Protease from Staphylococcus aureus.
Plos One, 8:e76812-e76812, 2013

PubMed Abstract: Staphylococcus aureus is a dangerous human pathogen. A number of the proteins secreted by this bacterium are implicated in its virulence, but many of the components of its secretome are poorly characterized. Strains of S. aureus can produce up to six homologous extracellular serine proteases grouped in a single spl operon. Although the SplA, SplB, and SplC proteases have been thoroughly characterized, the properties of the other three enzymes have not yet been investigated. Here, we describe the biochemical and structural characteristics of the SplD protease. The active enzyme was produced in an Escherichia coli recombinant system and purified to homogeneity. P1 substrate specificity was determined using a combinatorial library of synthetic peptide substrates showing exclusive preference for threonine, serine, leucine, isoleucine, alanine, and valine. To further determine the specificity of SplD, we used high-throughput synthetic peptide and cell surface protein display methods. The results not only confirmed SplD preference for a P1 residue, but also provided insight into the specificity of individual primed- and non-primed substrate-binding subsites. The analyses revealed a surprisingly narrow specificity of the protease, which recognized five consecutive residues (P4-P3-P2-P1-P1') with a consensus motif of R-(Y/W)-(P/L)-(T/L/I/V)↓S. To understand the molecular basis of the strict substrate specificity, we crystallized the enzyme in two different conditions, and refined the structures at resolutions of 1.56 Å and 2.1 Å. Molecular modeling and mutagenesis studies allowed us to define a consensus model of substrate binding, and illustrated the molecular mechanism of protease specificity.

PubMed: 24130791
DOI: 10.1371/journal.pone.0076812

Experimental method

X-RAY DIFFRACTION (1.56 Å)