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Literature summary extracted from

  • Tran, H.T.; Hong, M.K.; Ngo, H.P.; Huynh, K.H.; Ahn, Y.J.; Wang, Z.; Kang, L.W.
    Structure of D-alanine-D-alanine ligase from Yersinia pestis nucleotide phosphate recognition by the serine loop (2016), Acta Crystallogr. Sect. D, 72, 12-21 .
    View publication on PubMed

Application

EC Number Application Comment Organism
6.3.2.4 drug development DDL is an important drug target for the development of antibacterial agents Yersinia pestis

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.3.2.4 gene dll, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Yersinia pestis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.3.2.4 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

EC Number Inhibitors Comment Organism Structure
6.3.2.4 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

EC Number Metals/Ions Comment Organism Structure
6.3.2.4 Mg2+ required Yersinia pestis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6.3.2.4 ATP + 2 D-alanine Yersinia pestis
-
 ADP + phosphate + D-alanyl-D-alanine
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
6.3.2.4 Yersinia pestis Q8ZIE7
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
6.3.2.4 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 and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.3.2.4 ATP + 2 D-alanine
-
 Yersinia pestis ADP + phosphate + D-alanyl-D-alanine
-
 ?
6.3.2.4 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

EC Number Subunits Comment Organism
6.3.2.4 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

EC Number Synonyms Comment Organism
6.3.2.4 Ddl
-
 Yersinia pestis
6.3.2.4 dll
-
 Yersinia pestis
6.3.2.4 dllB
-
 Yersinia pestis
6.3.2.4 YpDDL
-
 Yersinia pestis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
6.3.2.4 37
-
 assay at Yersinia pestis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.3.2.4 7.8
-
 assay at Yersinia pestis

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.4 ATP
-
 Yersinia pestis

General Information

EC Number General Information Comment Organism
6.3.2.4 evolution conserved DDL structures consist of three domains: the N-terminal, central and C-terminal domains Yersinia pestis
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 Yersinia pestis
6.3.2.4 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