4KWB

Structure of signal peptide peptidase A with C-termini bound in the active sites: insights into specificity, self-processing and regulation

Summary for 4KWB

• Entry DOI: 10.2210/pdb4kwb/pdb
• Related: 3BEZ 3BFO 3RST
• Descriptor: Signal peptide peptidase SppA (2 entities in total)
• Functional Keywords: hydrolase, alpha/beta protein fold, signal peptide digestion, bacterial cell membrane, self-compartmentalized
• Biological source: Bacillus subtilis subsp. subtilis
• Cellular location: Cell membrane ; Single-pass membrane protein : O34525
• Total number of polymer chains: 8
• Total formula weight: 240033.14

Authors

Nam, S.E.,Paetzel, M. (deposition date: 2013-05-23, release date: 2013-11-27, Last modification date: 2023-09-20)

Primary citation

Nam, S.E.,Paetzel, M.
Structure of signal peptide peptidase A with C-termini bound in the active sites: insights into specificity, self-processing, and regulation.
Biochemistry, 52:8811-8822, 2013

PubMed Abstract: Bacterial signal peptide peptidase A (SppA) is a membrane-bound enzyme that utilizes a serine/lysine catalytic dyad mechanism to cleave remnant signal peptides within the cellular membrane. Bacillus subtilis SppA (SppABS) oligomerizes into a homo-octameric dome-shaped complex with eight active sites, located at the interface between each protomer. In this study, we show that SppABS self-processes its own C-termini. We have determined the crystal structure of a proteolytically stable fragment of SppABSK199A that has its C-terminal peptide bound in each of the eight active sites, creating a perfect circle of peptides. Substrate specificity pockets S1, S3, and S2' are identified and accommodate C-terminal residues Tyr331, Met329, and Tyr333, respectively. Tyr331 at the P1 position is conserved among most Bacillus species. The structure reveals that the C-terminus binds within the substrate-binding grooves in an antiparallel β-sheet fashion. We show, by C-terminal truncations, that the C-terminus is not essential for oligomeric assembly. Kinetic analysis shows that a synthetic peptide corresponding to the C-terminus of SppABS competes with a fluorometric peptide substrate for the SppABS active site. A model is proposed for how the C-termini of SppA may function in the regulation of this membrane-bound self-compartmentalized protease.

PubMed: 24228759
DOI: 10.1021/bi4011489

Experimental method

X-RAY DIFFRACTION (2.39 Å)