6FQB

MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae.

Morlot, C.Straume, D.Peters, K.Hegnar, O.A.Simon, N.Villard, A.M.Contreras-Martel, C.Leisico, F.Breukink, E.Gravier-Pelletier, C.Le Corre, L.Vollmer, W.Pietrancosta, N.Havarstein, L.S.Zapun, A.

(2018) Nat Commun 9: 3180-3180

  • DOI: 10.1038/s41467-018-05602-w
  • Primary Citation of Related Structures:  
    6FQB

  • PubMed Abstract: 
  • The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In ...

    The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France. andre.zapun@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mur ligase family proteinABCD465Streptococcus pneumoniaeMutation(s): 0 
Gene Names: A4260_05845ERS019420_00606ERS020535_00125ERS021368_00525ERS022199_00743ERS043879_01366
EC: 6.3.2 (PDB Primary Data), 6.3.5.13 (UniProt)
Find proteins for Q8DNZ9 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DNZ9 
Go to UniProtKB:  Q8DNZ9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cobyric acid synthaseEFGH260Streptococcus pneumoniaeMutation(s): 0 
Gene Names: 
EC: 6.3.5.10 (PDB Primary Data), 6.3.5.13 (UniProt), 3.5.1.2 (UniProt)
Find proteins for Q8DNZ8 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DNZ8 
Go to UniProtKB:  Q8DNZ8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download CCD File 
E, F, G, H
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 288.43α = 90
b = 288.43β = 90
c = 115.1γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
INSERM-Astra ZenecaFrance--

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection