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Literature summary extracted from

  • Huynh, K.H.; Hong, M.K.; Lee, C.; Tran, H.T.; Lee, S.H.; Ahn, Y.J.; Cha, S.S.; Kang, L.W.
    The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding (2015), J. Microbiol., 53, 776-782 .
    View publication on PubMed

Application

EC Number Application Comment Organism
6.3.2.4 drug development the enzyme is a target for drug development. Acinetobacter baumannii is emerging as a multidrug-resistant nosocomial pathogen, that causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections Acinetobacter baumannii

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.3.2.4 purified recombinant enzyme, development of several different crystallization conditions for the AbDDL protein, e.g. sitting drop vapor diffusion method, 14°C, by mixing of 0.06 M MgCl2 and CaCl2, 0.1 M imidazole, 2-(N-morpholino)ethanesulfonic acid-HCl, pH 6.5, with 30% of the precipitant EDO-P8K containing 40% v/v ethylene glycol and 20% w/v PEG 8000, or by microbatch method with 0.2 M NaSCN and 20% w/v PEG 3350 as crystallization solution, X-ray diffraciton structure determination and analysis at 2.2 A resolution, molecular replacement wit the DDL crystal structure from Yestis pestis as a template, PDB ID 3v4z Acinetobacter baumannii

Inhibitors

EC Number Inhibitors Comment Organism Structure
6.3.2.4 3-chloro-2,2-dimethyl-N-[4-(trifluoromethyl)phenyl]propanamide binding structure, overview Acinetobacter baumannii
6.3.2.4 D-cycloserine
-
 Acinetobacter baumannii
6.3.2.4 additional information proposed inhibitor binding site structure, overview Acinetobacter baumannii
6.3.2.4 phosphorylated D-ala-D-alpha-hydroxybutyrate phosphonate binding structure, overview Acinetobacter baumannii

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
6.3.2.4 additional information
-
 additional information steady-state kinetics of the Michaelis-Menten equation with a single binding site Acinetobacter baumannii
6.3.2.4 0.008
-
 D-alanine pH 7.8, 45°C, first D-Ala Acinetobacter baumannii
6.3.2.4 1.7
-
 ATP pH 7.8, 45°C, first D-Ala Acinetobacter baumannii
6.3.2.4 2.7
-
 D-alanine pH 7.8, 45°C, second D-Ala Acinetobacter baumannii

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.3.2.4 Mg2+ required Acinetobacter baumannii

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 Acinetobacter baumannii
-
 ADP + phosphate + D-alanyl-D-alanine
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
6.3.2.4 Acinetobacter baumannii
-
-
-

Substrates and Products (Substrate)

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

Subunits

EC Number Subunits Comment Organism
6.3.2.4 More the asymmetric unit contains six protomers of AbDDL. Five protomers have a closed conformation in the central domain, while one protomer has an open conformation in the central domain. The central domain with an open conformation does not interact with crystallographic symmetry-related protomers and the conformational change of the central domain is not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. Active site structure determination and comparison, closed and open conformations of the central domain, overview Acinetobacter baumannii

Synonyms

EC Number Synonyms Comment Organism
6.3.2.4 AbDDL
-
 Acinetobacter baumannii
6.3.2.4 Ddl
-
 Acinetobacter baumannii

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
6.3.2.4 45
-
 assay at Acinetobacter baumannii

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
6.3.2.4 30.08
-
 D-alanine pH 7.8, 45°C Acinetobacter baumannii

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.3.2.4 7.8
-
 assay at Acinetobacter baumannii

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.4 ATP the interdomain crevice between the central domain and the C-terminal domain contains the conserved nucleotide binding site, nucleotide binding site structure, overveiw Acinetobacter baumannii

General Information

EC Number General Information Comment Organism
6.3.2.4 additional information the crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity. The conformational change does not result from crystal packing. The central domain is connected to the N-terminal and C-terminal domains through two parallel loops Acinetobacter baumannii
6.3.2.4 physiological function the D-alanine-D-alanine ligase (DDL) catalyzes the ATP-dependent synthesis of D-alanyl-D-alanine. D-Ala-D-ala is a key component of the bacterial cell wall and it maintains cell wall stability through cross-linking the peptide chain of peptidoglycan Acinetobacter baumannii

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
6.3.2.4 11.14
-
 D-alanine pH 7.8, 45°C, second D-Ala Acinetobacter baumannii
6.3.2.4 3760.4
-
 D-alanine pH 7.8, 45°C, first D-Ala Acinetobacter baumannii