6KYD

Structure of the R217A mutant of Clostridium difficile sortase B

Summary for 6KYD

• Entry DOI: 10.2210/pdb6kyd/pdb
• Descriptor: Putative peptidase C60B, sortase B (1 entity in total)
• Functional Keywords: sortase b, cysteine transpeptidase, clostridium difficile, hydrolase
• Biological source: Clostridioides difficile 630
• Total number of polymer chains: 1
• Total formula weight: 26103.17

Authors

Kang, C.Y.,Huang, I.H.,Wu, T.Y.,Chang, J.C.,Hsiao, Y.Y.,Cheng, C.H.,Tsai, W.J.,Hsu, K.C.,Wang, S.Y. (deposition date: 2019-09-18, release date: 2020-02-19, Last modification date: 2023-11-22)

Primary citation

Kang, C.Y.,Huang, I.H.,Chou, C.C.,Wu, T.Y.,Chang, J.C.,Hsiao, Y.Y.,Cheng, C.H.,Tsai, W.J.,Hsu, K.C.,Wang, S.
Functional analysis ofClostridium difficilesortase B reveals key residues for catalytic activity and substrate specificity.
J.Biol.Chem., 295:3734-3745, 2020

PubMed Abstract: Most of Gram-positive bacteria anchor surface proteins to the peptidoglycan cell wall by sortase, a cysteine transpeptidase that targets proteins displaying a cell wall sorting signal. Unlike other bacteria, , the major human pathogen responsible for antibiotic-associated diarrhea, has only a single functional sortase (SrtB). Sortase's vital importance in bacterial virulence has been long recognized, and sortase B (Cd-SrtB) has become an attractive therapeutic target for managing infection. A better understanding of the molecular activity of Cd-SrtB may help spur the development of effective agents against infection. In this study, using site-directed mutagenesis, biochemical and biophysical tools, LC-MS/MS, and crystallographic analyses, we identified key residues essential for Cd-SrtB catalysis and substrate recognition. To the best of our knowledge, we report the first evidence that a conserved serine residue near the active site participates in the catalytic activity of Cd-SrtB and also SrtB from The serine residue indispensable for SrtB activity may be involved in stabilizing a thioacyl-enzyme intermediate because it is neither a nucleophilic residue nor a substrate-interacting residue, based on the LC-MS/MS data and available structural models of SrtB-substrate complexes. Furthermore, we also demonstrated that residues 163-168 located on the β6/β7 loop of Cd-SrtB dominate specific recognition of the peptide substrate PPKTG. The results of this work reveal key residues with roles in catalysis and substrate specificity of Cd-SrtB.

PubMed: 32005667
DOI: 10.1074/jbc.RA119.011322

Experimental method

X-RAY DIFFRACTION (3.1 Å)