7F8P

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with new carbapenem drug T203


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Allosteric cooperation in ss-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 ß-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 ß-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by ß-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 ß-lactam molecule and influences binding at the catalytic site. We provide evidence that two ß-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual ß-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./em>.


    Organizational Affiliation

    Medicine, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
59I (Subject of Investigation/LOI)
Query on 59I

Download Ideal Coordinates CCD File 
C [auth A](2R,3R)-3-methyl-4-(2-oxidanylidene-2-propan-2-yloxy-ethyl)sulfanyl-2-[(2R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2,3-dihydro-1H-pyrrole-5-carboxylic acid
C15 H23 N O6 S
BCFABNCZHGBALS-QARRAHMOSA-N
 Ligand Interaction
56X (Subject of Investigation/LOI)
Query on 56X

Download Ideal Coordinates CCD File 
G [auth A](4R,5S,6S)-6-((R)-1-hydroxyethyl)-3-((2-isopropoxy-2-oxoethyl)thio)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid
C15 H21 N O6 S
ZNVHAIJDJMRLJY-YJFSRANCSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
E [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.799α = 90
b = 94.278β = 93.136
c = 75.707γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report




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