5DU7

Crystal structure of ldtMt2 at 1.79 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Non-classical transpeptidases yield insight into new antibacterials.

Kumar, P.Kaushik, A.Lloyd, E.P.Li, S.G.Mattoo, R.Ammerman, N.C.Bell, D.T.Perryman, A.L.Zandi, T.A.Ekins, S.Ginell, S.L.Townsend, C.A.Freundlich, J.S.Lamichhane, G.

(2017) Nat. Chem. Biol. 13: 54-61

  • DOI: 10.1038/nchembio.2237
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial survival requires an intact peptidoglycan layer, a three-dimensional exoskeleton that encapsulates the cytoplasmic membrane. Historically, the final steps of peptidoglycan synthesis are known to be carried out by D,D-transpeptidases, enzyme ...

    Bacterial survival requires an intact peptidoglycan layer, a three-dimensional exoskeleton that encapsulates the cytoplasmic membrane. Historically, the final steps of peptidoglycan synthesis are known to be carried out by D,D-transpeptidases, enzymes that are inhibited by the β-lactams, which constitute >50% of all antibacterials in clinical use. Here, we show that the carbapenem subclass of β-lactams are distinctly effective not only because they inhibit D,D-transpeptidases and are poor substrates for β-lactamases, but primarily because they also inhibit non-classical transpeptidases, namely the L,D-transpeptidases, which generate the majority of linkages in the peptidoglycan of mycobacteria. We have characterized the molecular mechanisms responsible for inhibition of L,D-transpeptidases of Mycobacterium tuberculosis and a range of bacteria including ESKAPE pathogens, and used this information to design, synthesize and test simplified carbapenems with potent antibacterial activity.


    Organizational Affiliation

    Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.,Departments of Pharmacology &Physiology and Medicine, Rutgers University Medical School, New Jersey, USA.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Collaborations in Chemistry, Fuquay-Varina, North Carolina, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L,D-transpeptidase 2
A, B, D, C
370Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: ldtB
EC: 2.3.2.-
Find proteins for O53223 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  O53223
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.644α = 89.04
b = 75.534β = 89.96
c = 94.143γ = 92.76
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited States1DP2OD008459-01

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references
  • Version 1.2: 2016-11-23
    Type: Database references
  • Version 1.3: 2016-12-28
    Type: Database references
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence