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Literature summary 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 .
    View publication on PubMed

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
5.1.1.13 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
5.1.1.13 8.275
-
L-aspartate pH 4.6, 60°C, recombinant enzyme Picrophilus torridus
5.1.1.13 11.11
-
D-Aspartate pH 4.6, 60°C, recombinant enzyme Picrophilus torridus

Localization

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

Natural Substrates/ Products (Substrates)

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

Organism

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

Purification (Commentary)

EC Number Purification (Comment) Organism
5.1.1.13 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

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
5.1.1.13 D-aspartate
-
Picrophilus torridus L-aspartate
-
r
5.1.1.13 D-aspartate
-
Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 L-aspartate
-
r
5.1.1.13 L-aspartate
-
Picrophilus torridus D-aspartate
-
r
5.1.1.13 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
5.1.1.13 L-aspartate
-
Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 D-aspartate
-
r
5.1.1.13 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
5.1.1.13 additional information Picrophilus torridus aspartate racemase is highly specific to aspartate Picrophilus torridus ?
-
?
5.1.1.13 additional information PtoAspR racemizes L- and D-Asp but has no effect on other amino acids tested Picrophilus torridus ?
-
?
5.1.1.13 additional information Picrophilus torridus aspartate racemase is highly specific to aspartate Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 ?
-
?
5.1.1.13 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

EC Number Subunits Comment Organism
5.1.1.13 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

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

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
5.1.1.13 60
-
-
Picrophilus torridus

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
5.1.1.13 30 70 recombinant enzyme, about 20% of maximal activity at 30°C and 70°C, profile overview Picrophilus torridus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
5.1.1.13 5.5
-
-
Picrophilus torridus

pH Range

EC Number pH Minimum pH Maximum Comment Organism
5.1.1.13 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

EC Number Cofactor Comment Organism Structure
5.1.1.13 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

EC Number Organism Comment pI Value Maximum pI Value
5.1.1.13 Picrophilus torridus
-
-
5.45

General Information

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