Unravelling the reaction mechanism of glutamate amidation in Staphylococcus aureus peptidoglycan

Francisco Miguel Piçarra Leisico, Mertens HD, PhD thesis, NOVA University Lisbon - (2022) URL

SASDM22 – Staphylococcus aureus lipid II isoglutaminyl synthase MurT:GatD complex

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
MWI(0) 79 kDa
MWexpected 78 kDa
VPorod 121 nm3
log I(s) 6.34×10-3 6.34×10-4 6.34×10-5 6.34×10-6
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD small angle scattering data  s, nm-1
ln I(s)
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD Guinier plot ln 6.34×10-3 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD Kratky plot 1.104 0 3 sRg
p(r)
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD pair distance distribution function Rg: 3.3 nm 0 Dmax: 10.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Staphylococcus aureus lipid II isoglutaminyl synthase MurT:GatD complex Rg histogram Rg, nm
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD EOM/RANCH model
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD EOM/RANCH model
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD EOM/RANCH model
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD EOM/RANCH model
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD EOM/RANCH model

log I(s)
 s, nm-1
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD PDB (PROTEIN DATA BANK) model

log I(s)
 s, nm-1
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD CORAL model

Synchrotron SAXS data from solutions of S. aureus MurT:GatD complex in 100 mM Tris-HCl, 500 mM NaCl, 10 mM MgCl2, pH 8.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 40.00 μl sample at 4.1 mg/ml was injected at a 0.75 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 20°C. 1200 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT (saMurT)
Mol. type   Protein
Organism   Staphylococcus aureus (strain COL)
Olig. state   Monomer
Mon. MW   49.3 kDa
 
UniProt   A0A0H2WZQ7 (2-437)
Sequence   FASTA
 
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD (saGatD)
Mol. type   Protein
Organism   Staphylococcus aureus (strain COL)
Olig. state   Monomer
Mon. MW   28.5 kDa
 
UniProt   A0A0H2WZ38 (1-243)
Sequence   FASTA
 
PDB ID   6GS2