2MTZ

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

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

  • DOI: 10.1021/ja5105987

  • 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 importa ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative L,D-transpeptidase YkuD
A
175Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ykuD
EC: 2.-.-.-
Find proteins for O34816 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34816
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
intact bacterial peptidoglycan
B, C, D, E, F, G
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMU
Query on AMU
Download SDF File 
Download CCD File 
E
BETA-N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-YVNCZSHWSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
API
Query on API
B, C, D, E, F, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
FGA
Query on FGA
B, C, D, E, F, G
D-gamma-peptide, C-delta linkingC5 H9 N O4

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DAL
Query on DAL
B, C, D, E, F, G
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release