5K69

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 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
408Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ldtB (lppS)
EC: 2.3.2.-
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  I6Y9J2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6QR
Query on 6QR

Download SDF File 
Download CCD File 
A, B
(2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
C18 H20 N2 O4 S
AXGRCXYYLJVWGE-PQRHUAHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.140α = 90.00
b = 94.150β = 93.20
c = 75.630γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1R21AI111739-01
National Institutes of Health/Office of the DirectorUnited States1DP2OD008459-01

Revision History 

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