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Literature summary extracted from

  • Doan, T.T.; Kim, J.K.; Ngo, H.P.; Tran, H.T.; Cha, S.S.; Min Chung, K.; Huynh, K.H.; Ahn, Y.J.; Kang, L.W.
    Crystal structures of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides (2014), Arch. Biochem. Biophys., 545C, 92-99.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.3.2.4 apo, ADP-bound, ATP-bound, and AMPPNP-bound enzyme, sitting drop vapor diffusion method, mixing of 0.0025 ml of protein solution with 00.0025 ml of reservoir solution containing 15% w/v PEG 4000, 0.1 M Tris, pH 8.5, and 0.2 M MgCl2 with 0.3 M dimethylethyl-(3-sulfopropyl)-ammonium, 14°C, 24 h, ligand-bound enzyme structures by soaking apoenzyme crystals in each nucleotide-containing reservoir solution, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement Xanthomonas oryzae

Inhibitors

EC Number Inhibitors Comment Organism Structure
6.3.2.4 EDTA 10 mM, complete inhibition Xanthomonas oryzae

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.3.2.4 Mg2+ required Xanthomonas oryzae

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 Xanthomonas oryzae
-
 ADP + phosphate + D-alanyl-D-alanine
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
6.3.2.4 Xanthomonas oryzae Q5H614 pv. oryzae
-

Substrates and Products (Substrate)

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

Synonyms

EC Number Synonyms Comment Organism
6.3.2.4 Ddl
-
 Xanthomonas oryzae

Temperature Optimum [°C]

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

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
6.3.2.4 7.8
-
 assay at Xanthomonas oryzae

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.4 ATP
-
 Xanthomonas oryzae

General Information

EC Number General Information Comment Organism
6.3.2.4 additional information catalytic role of mega-loop, which contains two residues, K259 and Y260, which are crucial in substrate binding Xanthomonas oryzae