6FBT

The X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex with the reaction product NAG-anhNAMpentapeptide

Summary for 6FBT

• Entry DOI: 10.2210/pdb6fbt/pdb
• Descriptor: Probable soluble lytic transglycosylase, NAG-anhNAMpentapeptide, PHOSPHATE ION, ... (6 entities in total)
• Functional Keywords: lytic transglycosylase, lyase
• Biological source: Pseudomonas aeruginosa; More
• Total number of polymer chains: 2
• Total formula weight: 71478.19

Authors

Batuecas, M.T.,Dominguez-Gil, T.,Hermoso, J.A. (deposition date: 2017-12-19, release date: 2018-04-18, Last modification date: 2024-01-31)

Primary citation

Lee, M.,Batuecas, M.T.,Tomoshige, S.,Dominguez-Gil, T.,Mahasenan, K.V.,Dik, D.A.,Hesek, D.,Millan, C.,Uson, I.,Lastochkin, E.,Hermoso, J.A.,Mobashery, S.
Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt ofPseudomonas aeruginosa.
Proc. Natl. Acad. Sci. U.S.A., 115:4393-4398, 2018

PubMed Abstract: β-Lactam antibiotics inhibit cell-wall transpeptidases, preventing the peptidoglycan, the major constituent of the bacterial cell wall, from cross-linking. This causes accumulation of long non-cross-linked strands of peptidoglycan, which leads to bacterial death. , a nefarious bacterial pathogen, attempts to repair this aberrantly formed peptidoglycan by the function of the lytic transglycosylase Slt. We document in this report that Slt turns over the peptidoglycan by both exolytic and endolytic reactions, which cause glycosidic bond scission from a terminus or in the middle of the peptidoglycan, respectively. These reactions were characterized with complex synthetic peptidoglycan fragments that ranged in size from tetrasaccharides to octasaccharides. The X-ray structure of the wild-type apo Slt revealed it to be a doughnut-shaped protein. In a series of six additional X-ray crystal structures, we provide insights with authentic substrates into how Slt is enabled for catalysis for both the endolytic and exolytic reactions. The substrate for the exolytic reaction binds Slt in a canonical arrangement and reveals how both the glycan chain and the peptide stems are recognized by the Slt. We document that the apo enzyme does not have a fully formed active site for the endolytic reaction. However, binding of the peptidoglycan at the existing subsites within the catalytic domain causes a conformational change in the protein that assembles the surface for binding of a more expansive peptidoglycan between the catalytic domain and an adjacent domain. The complexes of Slt with synthetic peptidoglycan substrates provide an unprecedented snapshot of the endolytic reaction.

PubMed: 29632171
DOI: 10.1073/pnas.1801298115

Experimental method

X-RAY DIFFRACTION (2.5 Å)