5E1I | pdb_00005e1i

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.225 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1038/nchembio.2237
  • Primary Citation Related Structures: 
    5DU7, 5DUJ, 5DVP, 5DZJ, 5DZP, 5E1G, 5E1I, 5E51, 5E5L, 5K69

  • 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, 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.

Macromolecule Content 

  • Total Structure Weight: 79.44 kDa 
  • Atom Count: 5,623 
  • Modeled Residue Count: 701 
  • Deposited Residue Count: 740 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L,D-transpeptidase 2
A, B
370Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ldtBlppSRv2518cRVBD_2518cP425_02624
EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6Y9J2 
Go to UniProtKB:  I6Y9J2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6Y9J2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6B8

Query on 6B8



Download:Ideal Coordinates CCD File
D [auth A](2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid
C11 H17 N O4 S
ASUOZXIKIDLJND-VRRGKTLJSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.225 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.183α = 90
b = 93.957β = 93.04
c = 75.391γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2016-11-23
    Changes: Database references
  • Version 1.3: 2016-12-28
    Changes: Database references
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-10-09
    Changes: Structure summary