The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide (PubMed:22291598, PubMed:30154570). The MurT subunit catalyzes the ATP-dependent amidation of D-glutamate residue of lipid II, converting it to an isoglutamine residue (PubMed:22291598). ATP + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H2O + L-glutamine = ADP + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-D-isoglutaminyl-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H(+) + L-glutamate + phosphate ATP + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = ADP + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-O-P-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-O-P-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + NH4(+) = beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-D-isoglutaminyl-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H(+) + phosphate Optimum pH is 7.5-7.8 for isoglutaminyl synthase activity. Cell wall biogenesis; peptidoglycan biosynthesis. Forms a heterodimer with GatD. Composed of two domains: a Mur ligase middle domain containing the canonical ATP binding site and a ribbon-type zinc finger, and a C-terminal Mur ligase domain. The GatD/MurT complex has an open, boomerang-shaped conformation in which GatD is docked onto one end of MurT. Both proteins contribute to the catalytic triad. The gatD-murT double mutant displays susceptibility to diverse carbapenem and cephalosporin beta-lactam antibiotics and shows increased susceptibility to plectasin. Belongs to the MurCDEF family. MurT subfamily.