Unravelling the reaction mechanism of glutamate amidation in Staphylococcus aureus peptidoglycan

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

SASDLZ9 – Streptococcus pneumoniae lipid II isoglutaminyl synthase MurT:GatD complex (no Zn2+)

Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
MWI(0) 83 kDa
MWexpected 81 kDa
VPorod 126 nm3
log I(s) 2.59×10-2 2.59×10-3 2.59×10-4 2.59×10-5
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 2.59×10-2 Rg: 3.0 nm 0 (3.0 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: 3.0 nm 0 Dmax: 10 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Streptococcus pneumoniae lipid II isoglutaminyl synthase MurT:GatD complex (no Zn2+) 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

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. pneumoniae MurT:GatD complex in 50 mM Hepes, 10 mM MgCl2, 500 mM NaCl, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 55.00 μl sample at 6.5 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 20°C. 900 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 (spMurT)
Mol. type   Protein
Organism   Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Olig. state   Monomer
Mon. MW   51.9 kDa
 
UniProt   Q8DNZ9 (1-447)
Sequence   FASTA
 
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD (spGatD)
Mol. type   Protein
Organism   Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Olig. state   Monomer
Mon. MW   29.2 kDa
 
UniProt   Q8DNZ8
Sequence   FASTA
 
PDB ID   6FQB
 
PDB ID   6FQB