Literature summary for 6.3.2.4 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.

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

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

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Xanthomonas oryzae

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + 2 D-alanine	Xanthomonas oryzae	-	ADP + phosphate + D-alanyl-D-alanine	-	?

Organism

Organism	UniProt	Comment	Textmining
Xanthomonas oryzae	Q5H614	pv. oryzae	-

Substrates and Products (Substrate)

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

Synonyms

Synonyms	Comment	Organism
Ddl	-	Xanthomonas oryzae

Temperature Optimum [°C]

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

pH Optimum

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

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Xanthomonas oryzae

General Information

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