Literature summary for 4.1.2.4 extracted from

Sakuraba, H.; Yoneda, K.; Yoshihara, K.; Satoh, K.; Kawakami, R.; Uto, Y.; Tsuge, H.; Takahashi, K.; Hori, H.; Ohshima, T.
Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-D-ribose-5-phosphate aldolase (2007), Appl. Environ. Microbiol., 73, 7427-7434.

Search for more literature for 4.1.2.4

Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli strain BL21(DE3)	Pyrobaculum aerophilum

Crystallization (Commentary)

Crystallization (Comment)	Organism
hanging drop vapour diffusion method with 20% (w/v) polyethylene glycol 1000, 0.2 M zinc acetate, and 0.1 M acetate buffer (pH 4.5)	Pyrobaculum aerophilum

Inhibitors

Inhibitors	Comment	Organism	Structure
acetaldehyde	the wild type enzyme is highly resistant to high concentrations of acetaldehyde, whereas the recombinant DERA is almost completely inactivated after a 2 h exposure at 25°C	Pyrobaculum aerophilum
acetaldehyde	the wild type enzyme is highly resistant to high concentrations of acetaldehyde	Thermotoga maritima

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.02	-	2-deoxy-D-ribose 5-phosphate	native enzyme at 25°C in 0.1 M imidazole-HCl (pH 6.5)	Thermotoga maritima
0.066	-	2-deoxy-D-ribose 5-phosphate	native enzyme at 25°C in 0.1 M sodium acetate (pH 6.0)	Pyrobaculum aerophilum
0.23	-	2-deoxy-D-ribose 5-phosphate	recombinant enzyme at 25°C in triethanolamine-HCl (pH 7.5)	Pyrobaculum aerophilum

Organism

Organism	UniProt	Comment	Textmining
Pyrobaculum aerophilum	-	-	-
Thermotoga maritima	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
Superdex 200 gel filtration and DEAE-Toyopearl column chromatography	Thermotoga maritima
Superdex 200 gel filtration and DEAE-Toyopearl column chromatography	Pyrobaculum aerophilum

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
0.25	-	native enzyme, at 25°C	Pyrobaculum aerophilum
1	-	native enzyme, at 25°C	Thermotoga maritima
58	-	recombinant enzyme, at 25°C	Pyrobaculum aerophilum

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
2-deoxy-D-ribose 5-phosphate	-	Thermotoga maritima	D-glyceraldehyde 3-phosphate + acetaldehyde	-	?
2-deoxy-D-ribose 5-phosphate	-	Pyrobaculum aerophilum	D-glyceraldehyde 3-phosphate + acetaldehyde	-	?

Subunits

Subunits	Comment	Organism
dimer	x-ray crystallography	Pyrobaculum aerophilum

Synonyms

Synonyms	Comment	Organism
2-deoxy-D-ribose-5-phosphate aldolase	-	Thermotoga maritima
2-deoxy-D-ribose-5-phosphate aldolase	-	Pyrobaculum aerophilum
DERA	-	Thermotoga maritima
DERA	-	Pyrobaculum aerophilum

Temperature Stability [°C]

Temperature Stability Minimum [°C]	Temperature Stability Maximum [°C]	Comment	Organism
90	100	retains full activity when heated for 10 min at 90°C, at 100°C the activity is largely unchanged	Pyrobaculum aerophilum
90	100	retains full activity when heated for 10 min at 90°C, at 100°C, however, the activity is almost completely lost	Thermotoga maritima

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
6	-	native enzyme	Pyrobaculum aerophilum
6.5	-	-	Thermotoga maritima
7	-	recombinant enzyme	Pyrobaculum aerophilum

pH Stability

pH Stability	pH Stability Maximum	Comment	Organism
5	11	the native enzyme is extremely pH stable and shows no loss of activity when heated for 30 min at 50°C at pH levels ranging from 5 to 11	Thermotoga maritima
5	11	the native enzyme is extremely pH stable and shows no loss of activity when heated for 30 min at 50°C at pH levels ranging from 5 to 11	Pyrobaculum aerophilum
5.5	-	the recombinant enzyme shows significant loss of activity at pH less than 5.5	Pyrobaculum aerophilum
10	-	the recombinant enzyme shows significant loss of activity at pH above 10	Pyrobaculum aerophilum

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.3	-	after 20 h at 25°C	Thermotoga maritima	acetaldehyde
0.3	-	after 20 h at 25°C	Pyrobaculum aerophilum	acetaldehyde

Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.

Release 2023.1 (January 2023)