6D4K

Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for the Interaction and Processing of beta-Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis.

Libreros-Zuniga, G.A.Dos Santos Silva, C.Salgado Ferreira, R.Dias, M.V.B.

(2019) ACS Infect Dis 5: 260-271

  • DOI: https://doi.org/10.1021/acsinfecdis.8b00244
  • Primary Citation of Related Structures:  
    6D4K, 6D51, 6D5A

  • PubMed Abstract: 

    Targeting Mycobacterium tuberculosis peptidoglycans with β-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. β-Lactams inhibit peptidoglycan synthases such as l,d-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 → 3 cross-links. M. tuberculosis encodes five l,d-transpeptidases (Ldt Mt1-5 ), of which Ldt Mt3 is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of Ldt Mt3 at 1.3 and 1.8 Å resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other Ldts Mt enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The Ldt Mt3 -faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only a β-OH-butyrate or an acetyl group (C 2 H 3 O) covalently attached to the enzyme remains, an observation that strongly supports the notion that Ldt Mt3 is inactivated by β-lactams. Docking simulations with intact β-lactams predicted key Ldt Mt3 residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of Ldt Mt3 for ten β-lactams belonging to four different classes, and imipenem had the highest inactivation constant. This work provides key insights into the structure, binding mechanisms, and degradation of β-lactams by Ldt Mt3 , which may be useful for the development of additional β-lactams with potential antitubercular activity.


  • Organizational Affiliation

    Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , Avenida Prof. Lineu Prestes , 1374 São Paulo , Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable L,D-transpeptidase 3261Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1433RVBD_1433P425_01489
EC: 2.3.2
UniProt
Find proteins for O06825 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06825 
Go to UniProtKB:  O06825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06825
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.122α = 90
b = 46.407β = 90
c = 112.575γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2015/09188-8

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description