3TX4

Crystal Structure of Mutant (C354A) M. tuberculosis LD-transpeptidase type 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Targeting the Cell Wall of Mycobacterium tuberculosis: Structure and Mechanism of L,D-Transpeptidase 2.

Erdemli, S.B.Gupta, R.Bishai, W.R.Lamichhane, G.Amzel, L.M.Bianchet, M.A.

(2012) Structure 20: 2103-2115

  • DOI: 10.1016/j.str.2012.09.016
  • Primary Citation of Related Structures:  3TUR, 3U1P, 3VAE
  • Also Cited By: 4Z7A, 4ZFQ, 5DC2, 5DCC

  • PubMed Abstract: 
  • With multidrug-resistant cases of tuberculosis increasing globally, better antibiotic drugs and novel drug targets are becoming an urgent need. Traditional β-lactam antibiotics that inhibit D,D-transpeptidases are not effective against mycobacteria, ...

    With multidrug-resistant cases of tuberculosis increasing globally, better antibiotic drugs and novel drug targets are becoming an urgent need. Traditional β-lactam antibiotics that inhibit D,D-transpeptidases are not effective against mycobacteria, in part because mycobacteria rely mostly on L,D-transpeptidases for biosynthesis and maintenance of their peptidoglycan layer. This reliance plays a major role in drug resistance and persistence of Mycobacterium tuberculosis (Mtb) infections. The crystal structure at 1.7 Å resolution of the Mtb L,D-transpeptidase Ldt(Mt2) containing a bound peptidoglycan fragment, reported here, provides information about catalytic site organization as well as substrate recognition by the enzyme. Based on our structural, kinetic, and calorimetric data, we propose a catalytic mechanism for Ldt(Mt2) in which both acyl-acceptor and acyl-donor substrates reach the catalytic site from the same, rather than different, entrances. Together, this information provides vital insights to facilitate development of drugs targeting this validated yet unexploited enzyme.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mycobacterium Tuberculosis LD-transpeptidase type 2
A, B
287Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)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: 2.32 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.784α = 90.00
b = 121.031β = 90.00
c = 122.626γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references
  • Version 1.2: 2012-12-26
    Type: Database references