Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.62 kDa 
• Atom Count: 1661 
• Modelled Residue Count: 193 
• Deposited Residue Count: 199 
• Unique protein chains: 2

2MTZ

Haddock model of Bacillus subtilis L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide

• PDB DOI: 10.2210/pdb2MTZ/pdb
• BMRB: 25192

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


• Deposited: 2014-09-02 Released: 2015-01-14 
• Deposition Author(s): Schanda, P., Triboulet, S., Laguri, C., Bougault, C., Ayala, I., Callon, M., Arthur, M., Simorre, J.

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 200 
• Conformers Submitted: 5 
• Selection Criteria: target function 

Literature

Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan.

Schanda, P., Triboulet, S., Laguri, C., Bougault, C.M., Ayala, I., Callon, M., Arthur, M., Simorre, J.P.

(2014) J Am Chem Soc 136: 17852-17860

• PubMed: 25429710 
• DOI: 10.1021/ja5105987
• Primary Citation of Related Structures:  
  2MTZ


• PubMed Abstract: 
  

The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.

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Organizational Affiliation: 

University Grenoble Alpes, IBS , F-38044 Grenoble, France.

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  Gene Names: BSU14040, Y647_14120, ykuD EC: 2
UniProt
Find proteins for O34816 (Bacillus subtilis (strain 168)) Explore O34816  Go to UniProtKB:  O34816

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
intact bacterial peptidoglycan	B, C, D, E, F, G	4	Bacillus subtilis	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid	H	12		N/A
Glycosylation Resources
GlyTouCan:  G68491YY GlyCosmos:  G68491YY

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
API	B, C, D, E, F, G	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 200 
• Conformers Submitted: 5 
• Selection Criteria: target function 
• OLDERADO: 2MTZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-09-02 
• Released Date: 2015-01-14 
Deposition Author(s): Schanda, P., Triboulet, S., Laguri, C., Bougault, C., Ayala, I., Callon, M., Arthur, M., Simorre, J.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary