6FQB | pdb_00006fqb

MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6

• PDB DOI: https://doi.org/10.2210/pdb6FQB/pdb

• Classification: LIGASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-02-13 Released: 2018-08-22 
• Deposition Author(s): Morlot, C., Contreras-Martel, C., Leisico, F., Straume, D., Peters, K., Hegnar, O.A., Simon, N., Villard, A.M., Breukink, E., Gravier-Pelletier, C., Le Corre, L., Vollmer, W., Pietrancosta, N., Havarstein, L.S., Zapun, A.
• Funding Organization(s): INSERM-Astra Zeneca

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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

• PubMed: 30093673 
• DOI: https://doi.org/10.1038/s41467-018-05602-w
• Primary Citation 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 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.

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Organizational Affiliation: 
• Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.
Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway.
Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom.
Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal.
Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands.
Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France.
Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 325.23 kDa 
• Atom Count: 19,727 
• Modeled Residue Count: 2,504 
• Deposited Residue Count: 2,900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mur ligase family protein	A, C [auth B], E [auth C], G [auth D]	465	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: A4260_05845, ERS019420_00606, ERS020535_00125, ERS021368_00525, ERS022199_00743, ERS043879_01366 EC: 6.3.2 (PDB Primary Data), 6.3.5.13 (UniProt)
UniProt
Find proteins for Q8DNZ9 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DNZ9  Go to UniProtKB:  Q8DNZ9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobyric acid synthase	B [auth E], D [auth F], F [auth G], H	260	Streptococcus pneumoniae	Mutation(s): 0  Gene Names:  A4260_05840, AWW74_09320, CHL72_09035, CIT24_04835, CS877_04020, CSH34_00860, ERS003549_02292, ERS019166_00428, ERS019416_00232, ERS019420_00605, ERS019499_01955, ERS019595_01427, ERS020136_01107, ERS020137_00292, ERS020140_00887, ERS020142_00808, ERS020143_01959, ERS020147_00746, ERS020148_00821, ERS020178_04008, ERS020408_00223, ERS020474_01302, ERS020521_00204, ERS020522_00778, ERS020523_00656, ERS020524_01042, ERS020526_00540, ERS020526_04035, ERS020527_01973, ERS020528_00148, ERS020541_00600, ERS020692_00332, ERS020827_01405, ERS020831_02169, ERS021300_01369, ERS021447_05442, ERS021629_07046, ERS021762_02260, ERS021858_02776, ERS022045_06260, ERS022071_00358, ERS022199_00742, ERS022232_05365, ERS022363_01901, ERS022390_00924, ERS044004_01668, ERS068943_01580, ERS232497_02277, ERS232498_04930, ERS232508_01880, ERS409064_00176, ERS558328_00424, SAMEA1026345_00620, SAMEA2626854_01213, SAMEA2626872_01126 EC: 6.3.5.10 (PDB Primary Data), 6.3.5.13 (UniProt), 3.5.1.2 (UniProt)
UniProt
Find proteins for Q8DNZ8 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DNZ8  Go to UniProtKB:  Q8DNZ8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLN	I [auth E], J [auth F], K [auth G], L [auth H]	GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.228 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 288.43	α = 90
b = 288.43	β = 90
c = 115.1	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Morlot, C., Contreras-Martel, C., Leisico, F., Straume, D., Peters, K., Hegnar, O.A., Simon, N., Villard, A.M., Breukink, E., Gravier-Pelletier, C., Le Corre, L., Vollmer, W., Pietrancosta, N., Havarstein, L.S., Zapun, A.

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Funding Organization	Location	Grant Number
INSERM-Astra Zeneca	France	--

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-11-07
  Changes: Data collection
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary