Application | Comment | Organism |
---|---|---|
drug development | DDL is an important drug target for the development of antibacterial agents | Yersinia pestis |
Cloned (Comment) | Organism |
---|---|
gene dll, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Yersinia pestis |
Crystallization (Comment) | Organism |
---|---|
purified enzyme in apoform, AMP-bound, ADP-bound, adenosine 5'-(beta,gamma-imido)triphosphate-bound, and D-alanyl-D-alanine, and ADP-bound structures, hanging drop vapour diffusion method, mixing of 900 nl of 8 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 20 mM NaCl, and 3 mM 2-mercaptoethanol, with 900 nl of reservoir solution containing 0.2 M sodium acetate, 0.1 M Bis-Tris, pH 7.0, and 29% PEG 8000, and equilibration against 1 ml of reservoir solution, 14°C, 2 days, method optimization, X-ray diffraction structure determination and analysis 1.7-2.5 A resolution, molecular replacement of the apoenzyme structure using a structure as model, PDB entry 3v4z | Yersinia pestis |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
Vancomycin | the antibiotic is primarily used against methicillin-resistant Staphylococcus, it recognizes the terminal D-Ala-D-Ala moiety of the peptide chain of peptidoglycan and inhibits the cross-linking of cell-wall peptidoglycan precursors, eventually causing bacterial cell lysis | Yersinia pestis |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Yersinia pestis |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + 2 D-alanine | Yersinia pestis | - |
ADP + phosphate + D-alanyl-D-alanine | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Yersinia pestis | Q8ZIE7 | - |
- |
Purification (Comment) | Organism |
---|---|
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, tag cleavage through TEV protease, and another step of nickel affinity chromatography, followed by desalting gel filtration, dialysis, and ultrafiltration | Yersinia pestis |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + 2 D-alanine | - |
Yersinia pestis | ADP + phosphate + D-alanyl-D-alanine | - |
? | |
additional information | substrate-binding mechanism of enzyme YpDDL involving conformational changes of the loops, overview. Two D-alanine-binding sites are located next to each other between the N-terminal domain and the C-terminal domain, and an ATP-binding site exists between the central and the C-terminal domains | Yersinia pestis | ? | - |
? |
Subunits | Comment | Organism |
---|---|---|
dimer | enzyme YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the omega-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the omega-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Two D-alanine-binding sites are located next to each other between the N-terminal domain and the C-terminal domain, and an ATP-binding site exists between the central and the C-terminal domains. Structure-function relationship analysis of the enzyme, overview | Yersinia pestis |
Synonyms | Comment | Organism |
---|---|---|
Ddl | - |
Yersinia pestis |
dll | - |
Yersinia pestis |
dllB | - |
Yersinia pestis |
YpDDL | - |
Yersinia pestis |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
37 | - |
assay at | Yersinia pestis |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.8 | - |
assay at | Yersinia pestis |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
ATP | - |
Yersinia pestis |
General Information | Comment | Organism |
---|---|---|
evolution | conserved DDL structures consist of three domains: the N-terminal, central and C-terminal domains | Yersinia pestis |
additional information | substrate-binding mechanism of enzyme YpDDL involving conformational changes of the loops, structure-function relationship analysis of the enzyme, overview | Yersinia pestis |
physiological function | D-alanyl-D-alanine ligase (DDL) catalyzes the formation of the dipeptide D-alanyl-D-alanine (D-Ala-D-Ala) in an ATP-dependent manner. D-alanyl-D-alanine is added to the peptide chain of peptidoglycan and is responsible for the stability of the bacterial cell wall | Yersinia pestis |