Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary for 6.3.2.4 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

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

Cloned(Commentary)

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

Crystallization (Commentary)

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

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

Metals/Ions Comment Organism Structure
Mg2+ required Yersinia pestis

Natural Substrates/ Products (Substrates)

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

Organism UniProt Comment Textmining
Yersinia pestis Q8ZIE7
-
-

Purification (Commentary)

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 and Products (Substrate)

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

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

Synonyms Comment Organism
Ddl
-
Yersinia pestis
dll
-
Yersinia pestis
dllB
-
Yersinia pestis
YpDDL
-
Yersinia pestis

Temperature Optimum [°C]

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

pH Optimum

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

Cofactor

Cofactor Comment Organism Structure
ATP
-
Yersinia pestis

General Information

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