EC Number |
General Information |
Reference |
---|
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 | more |
catalytic role of mega-loop, which contains two residues, K259 and Y260, which are crucial in substrate binding |
726822 |
6.3.2.4 | more |
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 | more |
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 | more |
NMR ligand binding assay for D-alanine-D-alanine ligase, overview |
-, 728209 |
6.3.2.4 | more |
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 | more |
substrate-binding mechanism of enzyme YpDDL involving conformational changes of the loops, structure-function relationship analysis of the enzyme, overview |
743944 |