6.3.2.4	evolution	conserved DDL structures consist of three domains: the N-terminal, central and C-terminal domains	743944	
6.3.2.4	evolution	phylogenetic tree based on the amino acid sequences of D-alanyl-D-alanine ligases (Ddls) in the proteomes of Escherichia coli and ddlR-positive bacteria, overview. DdlR-mediated transcriptional regulation of ddlR and ddl may occur in multiple bacterial systems such as Actinobacteria and Bacillus species	-, 744879	
6.3.2.4	malfunction	inhibition of Ddl prevents bacterial growth	728577	
6.3.2.4	metabolism	two different metabolic pathways, of DdlA and LysA, respectively, leading to peptidoglycan biosynthesis, overview	-, 745827	
6.3.2.4	additional information	catalytic role of mega-loop, which contains two residues, K259 and Y260, which are crucial in substrate binding	726822	
6.3.2.4	additional information	comparative molecular modeling approach for SsDdl, enzyme structure homology modeling using the Ddl structure mdoel of Streptococcus mutans (SmDdl) as template, PDB ID 3K3P, overview	-, 745681	
6.3.2.4	additional information	homology structure modeling analyses of wild-type enzyme and mutants S293D and S293E. Both amino acids Arg268 and Ser293 play an important role in the synthesis of D-Ala-D-Ala, residue Ser293 recognizes the carboxylate group of D-Ala2, but is not involved in the ATP hydrolysis, while the Arg268 residue recognizes the carboxylate group of D-Ala1 and is involved in ATP hydrolysis to form the activated acyl-phosphate intermediate. Ligand docking simulations	-, 745494	
6.3.2.4	additional information	NMR ligand binding assay for D-alanine-D-alanine ligase, overview	-, 728209	
6.3.2.4	additional information	Phe261 is a key specificity determinant in the alpha-helical cap of the Omega-loop when folded into the closed conformation, molecular docking, overview. The hydroxyl of Tyr261 plays an instrumental role in determining non-productive docking orientations of dlactate, i.e. D-lactate-OH as an H-bond donor to the Tyr261-OH or D-lactate as an H-bond donor to the phosphoryl of the intermediate D-alanyl phosphate, and the D-lactate-COO- as an H-bond acceptor for the Tyr261-OH. Arg301 is required for the activation of the nucleophilic D-lactate for D-Ala-D-lactate formation. Ligand binding docking structure study, involving also the transition-state analogue, overview	728168	
6.3.2.4	additional information	substrate-binding mechanism of enzyme YpDDL involving conformational changes of the loops, structure-function relationship analysis of the enzyme, overview	743944