Literature summary for 1.4.99.6 extracted from

Fu, G.; Yuan, H.; Li, C.; Lu, C.D.; Gadda, G.; Weber, I.T.
Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase (2010), Biochemistry, 49, 8535-8545.

Crystallization (Commentary)

Crystallization (Comment)	Organism
in complex with iminoarginine, to 1.06 A resolution, and in complex with iminohistidine, to 1.3 A resolution. The structure comprises an unliganded conformation and a product-bound conformation. The active site is partially occupied with iminoarginine product that interacts with Tyr53 in the minor conformation of a surface loop. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In complex with iminohistidine, two alternate conformations are observed for iminohistidine where the imidazole groups form hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000fold difference in kcat/Km values for D-arginine and D-histidine	Pseudomonas aeruginosa

Crystallization (Comment)

Organism

in complex with iminoarginine, to 1.06 A resolution, and in complex with iminohistidine, to 1.3 A resolution. The structure comprises an unliganded conformation and a product-bound conformation. The active site is partially occupied with iminoarginine product that interacts with Tyr53 in the minor conformation of a surface loop. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In complex with iminohistidine, two alternate conformations are observed for iminohistidine where the imidazole groups form hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000fold difference in kcat/Km values for D-arginine and D-histidine

Pseudomonas aeruginosa

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.06	-	D-arginine	pH 8.7, 25°C	Pseudomonas aeruginosa
0.26	-	D-Lysine	pH 8.7, 25°C	Pseudomonas aeruginosa
0.8	-	D-tyrosine	pH 8.7, 25°C	Pseudomonas aeruginosa
10	-	D-methionine	pH 8.7, 25°C	Pseudomonas aeruginosa
11	-	D-phenylalanine	pH 8.7, 25°C	Pseudomonas aeruginosa
11	-	D-histidine	pH 8.7, 25°C	Pseudomonas aeruginosa
12	-	D-leucine	pH 8.7, 25°C	Pseudomonas aeruginosa

Organism

Organism	UniProt	Comment	Textmining
Pseudomonas aeruginosa	Q9HXE3	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
D-arginine + phenazine methosulfate	-	Pseudomonas aeruginosa	5-guanidino-2-oxopentanoate + NH3 + reduced phenazine methosulfate	overall reaction	?
D-histidine + phenazine methosulfate	-	Pseudomonas aeruginosa	3-(1H-imidazol-4-yl)-2-oxopropanoate + NH3 + reduced phenazine methosulfate	overall reaction	?
D-leucine + phenazine methosulfate	-	Pseudomonas aeruginosa	? + NH3 + reduced phenazine methosulfate	overall reaction	?
D-lysine + phenazine methosulfate	-	Pseudomonas aeruginosa	6-amino-2-oxohexanoate + NH3 + reduced phenazine methosulfate	overall reaction	?
D-methionine + phenazine methosulfate	-	Pseudomonas aeruginosa	4-methylsulfanyl-2-oxobutanoate + NH3 + reduced phenazine methosulfate	overall reaction	?
D-phenylalanine + phenazine methosulfate	-	Pseudomonas aeruginosa	2-oxo-3-phenylpropanoate + NH3 + reduced phenazine methosulfate	overall reaction	?
D-tyrosine + phenazine methosulfate	-	Pseudomonas aeruginosa	3-(4-hydroxyphenyl)-2-oxopropanoate + NH3 + reduced phenazine methosulfate	overall reaction	?

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
6.4	-	D-leucine	pH 8.7, 25°C	Pseudomonas aeruginosa
23	-	D-tyrosine	pH 8.7, 25°C	Pseudomonas aeruginosa
35	-	D-histidine	pH 8.7, 25°C	Pseudomonas aeruginosa
75	-	D-phenylalanine	pH 8.7, 25°C	Pseudomonas aeruginosa
141	-	D-Lysine	pH 8.7, 25°C	Pseudomonas aeruginosa
154	-	D-methionine	pH 8.7, 25°C	Pseudomonas aeruginosa
204	-	D-arginine	pH 8.7, 25°C	Pseudomonas aeruginosa

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.515	-	D-leucine	pH 8.7, 25°C	Pseudomonas aeruginosa
3.14	-	D-histidine	pH 8.7, 25°C	Pseudomonas aeruginosa
6.9	-	D-phenylalanine	pH 8.7, 25°C	Pseudomonas aeruginosa
14.8	-	D-methionine	pH 8.7, 25°C	Pseudomonas aeruginosa
27.6	-	D-tyrosine	pH 8.7, 25°C	Pseudomonas aeruginosa
530	-	D-Lysine	pH 8.7, 25°C	Pseudomonas aeruginosa
3400	-	D-arginine	pH 8.7, 25°C	Pseudomonas aeruginosa