4A52

NMR structure of the imipenem-acylated L,D-transpeptidase from Bacillus subtilis

Summary for 4A52

• Entry DOI: 10.2210/pdb4a52/pdb
• Related: 1Y7M 3ZQD 4A1I 4A1J 4A1K
• NMR Information: BMRB: 18037
• Descriptor: PUTATIVE L, D-TRANSPEPTIDASE YKUD, (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid (2 entities in total)
• Functional Keywords: transferase, peptidoglycan, antibiotic resistance, cysteine protease
• Biological source: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
• Cellular location: Spore wall : O34816
• Total number of polymer chains: 1
• Total formula weight: 19262.09

Authors

Lecoq, L.,Simorre, J.,Bougault, C.,Arthur, M.,Hugonnet, J.,Veckerle, C.,Pessey, O. (deposition date: 2011-10-24, release date: 2012-05-30, Last modification date: 2024-10-23)

Primary citation

Lecoq, L.,Bougault, C.,Hugonnet, J.,Veckerle, C.,Pessey, O.,Arthur, M.,Simorre, J.P.
Dynamics Induced by Beta-Lactam Antibiotics in the Active Site of Bacillus subtilis L,D-Transpeptidase.
Structure, 20:850-861, 2012

PubMed Abstract: β-lactams inhibit peptidoglycan polymerization by acting as suicide substrates of essential d,d-transpeptidases. Bypass of these enzymes by unrelated l,d-transpeptidases results in β-lactam resistance, although carbapenems remain unexpectedly active. To gain insight into carbapenem specificity of l,d-transpeptidases (Ldts), we solved the nuclear magnetic resonance (NMR) structures of apo and imipenem-acylated Bacillus subtilis Ldt and show that the cysteine nucleophile is present as a neutral imidazole-sulfhydryl pair in the substrate-free enzyme. NMR relaxation dispersion does not reveal any preexisting conformational exchange in the apoenzyme, and change in flexibility is not observed upon noncovalent binding of β-lactams (K(D) > 37.5 mM). In contrast, covalent modification of active cysteine by both carbapenems and 2-nitro-5-thiobenzoate induces backbone flexibility that does not result from disruption of the imidazole-sulfhydryl proton interaction or steric hindrance. The chemical step of the reaction determines enzyme specificity since no differences in drug affinity were observed.

PubMed: 22579252
DOI: 10.1016/J.STR.2012.03.015

Experimental method

SOLUTION NMR