Literature summary for 5.1.1.13 extracted from

Aihara, T.; Ito, T.; Yamanaka, Y.; Noguchi, K.; Odaka, M.; Sekine, M.; Homma, H.; Yohda, M.
Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus (2016), Extremophiles, 20, 385-393 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant enzyme expression in Escherichia coli strain BL21(DE3)	Picrophilus torridus

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme, vapour diffusion method, mixing of 8-12 mg/ml protein in 50 mM Tris-HCl, pH 8.0, with reservoir solution containing 20-25% w/v PEG 3400, 200 mM potassium/sodium tartrate, and 1 mM L-aspartate, X-ray diffraction structure determination and analysis at 1.85 A resolution, molecular replacement method using the structure of aspartate racemase from Salmonella typhimurium, PDB ID 3S81, as a probe model	Picrophilus torridus

Crystallization (Comment)

Organism

purified recombinant enzyme, vapour diffusion method, mixing of 8-12 mg/ml protein in 50 mM Tris-HCl, pH 8.0, with reservoir solution containing 20-25% w/v PEG 3400, 200 mM potassium/sodium tartrate, and 1 mM L-aspartate, X-ray diffraction structure determination and analysis at 1.85 A resolution, molecular replacement method using the structure of aspartate racemase from Salmonella typhimurium, PDB ID 3S81, as a probe model

Picrophilus torridus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
8.275	-	L-aspartate	pH 4.6, 60°C, recombinant enzyme	Picrophilus torridus
11.11	-	D-Aspartate	pH 4.6, 60°C, recombinant enzyme	Picrophilus torridus

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
cytosol	-	Picrophilus torridus	5829	-

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
L-aspartate	Picrophilus torridus	-	D-aspartate	-	r
L-aspartate	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	-	D-aspartate	-	r
additional information	Picrophilus torridus	Picrophilus torridus aspartate racemase is highly specific to aspartate	?	-	?
additional information	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	Picrophilus torridus aspartate racemase is highly specific to aspartate	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Picrophilus torridus	Q6L2R8	-	-
Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	Q6L2R8	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant enzyme from Escherichia coli strain BL21(DE3) by ammonium sulfate fractionation, hydrophobic interaction chromatography, dialysis anion change chromatography, and ultrafiltration	Picrophilus torridus

Source Tissue

Source Tissue	Comment	Organism	Textmining
additional information	the optimal growth temperature is about 60°C	Picrophilus torridus	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
D-aspartate	-	Picrophilus torridus	L-aspartate	-	r
D-aspartate	-	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	L-aspartate	-	r
L-aspartate	-	Picrophilus torridus	D-aspartate	-	r
L-aspartate	the aspartate racemase exhibits high substrate specificity to aspartate, L- to D-aspartate is the preferred reaction direction	Picrophilus torridus	D-aspartate	-	r
L-aspartate	-	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	D-aspartate	-	r
L-aspartate	the aspartate racemase exhibits high substrate specificity to aspartate, L- to D-aspartate is the preferred reaction direction	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	D-aspartate	-	r
additional information	Picrophilus torridus aspartate racemase is highly specific to aspartate	Picrophilus torridus	?	-	?
additional information	PtoAspR racemizes L- and D-Asp but has no effect on other amino acids tested	Picrophilus torridus	?	-	?
additional information	Picrophilus torridus aspartate racemase is highly specific to aspartate	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	?	-	?
additional information	PtoAspR racemizes L- and D-Asp but has no effect on other amino acids tested	Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828	?	-	?

Subunits

Subunits	Comment	Organism
homodimer	comparisons of Picrophilus torridus enzyme structure with the Pyrococcus aspartate racemase structure. The dimerization interface is composed of three interaction surfaces, including an inter-subunit disulfide bond and contacts through the beta-sheets and alpha-helix. The interface between two molecules (Mol-A and Mol-B) of Picrophilus torridus PtoAspR looks similar to that of Pyrococcus aspartate racemase, except that there is no cysteine disulfide bond between two molecules of PtoAspR. Each subunit is composed of two homologous domains, the N-terminal domain with residues 1-101 and 207-232, and the C-terminal domain with residues 106-206. The putative catalytic residues, Arg49, Cys83, Asn84, Thr85, Lys159, Cys188, Thr189, are located in the pocket between two domains	Picrophilus torridus

Synonyms

Synonyms	Comment	Organism
PTO0149	locus name	Picrophilus torridus
PtoAspR	-	Picrophilus torridus
pyridoxal 5'-phosphate-independent aspartate racemase	-	Picrophilus torridus

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
60	-	-	Picrophilus torridus

Temperature Range [°C]

Temperature Minimum [°C]	Temperature Maximum [°C]	Comment	Organism
30	70	recombinant enzyme, about 20% of maximal activity at 30°C and 70°C, profile overview	Picrophilus torridus

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
5.5	-	-	Picrophilus torridus

pH Range

pH Minimum	pH Maximum	Comment	Organism
4.6	6.5	recombinant enzyme, the activity at pH 4.6 is approximately 6times lower than that at the optimal pH 5.5. The activity is completely lost at approximately pH 4.0, 50% of maximal actiivty at pH 6.5, profile overview	Picrophilus torridus

Cofactor

Cofactor	Comment	Organism	Structure
additional information	a pyridoxal 5'-phosphate-independent aspartate racemase. The putative catalytic residues, Arg49, Cys83, Asn84, Thr85, Lys159, Cys188, Thr189, are located in the pocket between two domains	Picrophilus torridus

pI Value

Organism	Comment	pI Value Maximum	pI Value
Picrophilus torridus	-	-	5.45

General Information

General Information	Comment	Organism
metabolism	because Picrophilus aspartate racemase is highly specific to aspartate, other amino acid racemases might exist in Picrophilus torridus	Picrophilus torridus