The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide (PubMed:24044435, PubMed:30093673). The GatD subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia. The resulting ammonia molecule is channeled to the active site of MurT (PubMed:30093673). 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 H2O + L-glutamine = L-glutamate + NH4(+) Cell wall biogenesis; peptidoglycan biosynthesis. Forms a heterodimer with MurT. Severe depletion of GatD/MurT produces a high proportion of aberrant cells, elongated or bulging. Belongs to the CobB/CobQ family. GatD subfamily.