5E51

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 with Faropenem adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.258 

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 1
A, B, C, D
223Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: ldtA
EC: 2.3.2.-
Find proteins for Q7DAG3 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  Q7DAG3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5KO
Query on 5KO

Download SDF File 
Download CCD File 
A, C
(3R)-3-hydroxybutanal
Faropenem adduct
C4 H8 O2
HSJKGGMUJITCBW-SCSAIBSYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.258 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 58.379α = 90.00
b = 58.379β = 90.00
c = 257.397γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
HKL-3000data collection

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: 2016-10-26
    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: 2017-09-13
    Type: Author supporting evidence