4A52 | pdb_00004a52

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

• PDB DOI: https://doi.org/10.2210/pdb4A52/pdb
• BMRB: 18037

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-24 Released: 2012-05-30 
• Deposition Author(s): Lecoq, L., Simorre, J., Bougault, C., Arthur, M., Hugonnet, J., Veckerle, C., Pessey, O.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: STRUCTURE WITH THE LOWEST ENERGY 

Literature

Dynamics Induced by Beta-Lactam Antibiotics in the Active Site of Bacillus subtilis L,D-Transpeptidase.

Lecoq, L., Bougault, C., Hugonnet, J., Veckerle, C., Pessey, O., Arthur, M., Simorre, J.P.

(2012) Structure 20: 850-861

• PubMed: 22579252 
• DOI: https://doi.org/10.1016/j.str.2012.03.015
• Primary Citation Related Structures: 
  3ZQD, 4A52


• 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.

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Organizational Affiliation: 
• CEA, DSV, Institut de Biologie Structurale (IBS), Grenoble F-38027, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.26 kDa 
• Atom Count: 1,296 
• Modeled Residue Count: 169 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE L, D-TRANSPEPTIDASE YKUD	A	175	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  EC: 2
UniProt
Find proteins for O34816 (Bacillus subtilis (strain 168)) Explore O34816  Go to UniProtKB:  O34816

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM2	B [auth A]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C12 H19 N3 O4 S UACUABDJLSUFFC-IWSPIJDZSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: STRUCTURE WITH THE LOWEST ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Lecoq, L., Simorre, J., Bougault, C., Arthur, M., Hugonnet, J., Veckerle, C., Pessey, O.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-07-11
  Changes: Other
• Version 1.2: 2014-01-15
  Changes: Database references, Structure summary
• Version 2.0: 2018-01-24
  Changes: Advisory, Atomic model, Data collection, Database references
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary