7F71

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase.

Ahmad, N.Dugad, S.Chauhan, V.Ahmed, S.Sharma, K.Kachhap, S.Zaidi, R.Bishai, W.R.Lamichhane, G.Kumar, P.

(2022) Elife 11

  • DOI: 10.7554/eLife.73055
  • Primary Citation of Related Structures:  
    7F71, 7F8P

  • PubMed Abstract: 
  • L,D-transpeptidase function predominates in atypical 3 → 3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis . Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or β-lactam antibiotics ...

    L,D-transpeptidase function predominates in atypical 3 → 3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis . Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or β-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by β-lactams. Here, we report identification of an allosteric site at a distance of 21 Å from the catalytic site that binds the sugar moiety of PG substrates (hereafter referred to as the S-pocket). This site also binds a second β-lactam molecule and influences binding at the catalytic site. We provide evidence that two β-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual β-lactam-binding phenomenon is previously unknown and is an observation that may offer novel approaches for the structure-based design of new drugs against M. tuberculosis .


    Organizational Affiliation

    Department of Infectious Diseases, Centre for Tuberculosis Research, Johns Hopkins University, Baltimore, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L,D-transpeptidase 2A, B370Mycobacterium 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.906α = 90
b = 93.981β = 92.975
c = 75.539γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaCRG/2019/005079
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR33 AI111739
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI137720

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references