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Literature summary for 1.13.11.4 extracted from

  • Li, N.; Peng, Q.; Yao, L.; He, Q.; Qiu, J.; Cao, H.; He, J.; Niu, Q.; Lu, Y.; Hui, F.
    Roles of the gentisate 1,2-dioxygenases DsmD and GtdA in the catabolism of the herbicide Dicamba in Rhizorhabdus dicambivorans Ndbn-20 (2020), J. Agric. Food Chem., 68, 9287-9298 .
    View publication on PubMed
Search for more literature for 1.13.11.4

Cloned(Commentary)

Cloned (Comment) Organism
overexpression of His6-tagged enzyme in Escherichia coli BL21(DE3) Rhizorhabdus dicambivorans

General Stability

General Stability Organism
the enzyme is very unstable and could not be purified in the absence of Fe2+ Rhizorhabdus dicambivorans

Inhibitors

Inhibitors Comment Organism Structure
Ag+ 1 mM, severely inhibited Rhizorhabdus dicambivorans
Al3+ 1 mM, moderately inhibited Rhizorhabdus dicambivorans
Cd2+ 1 mM, severely inhibited Rhizorhabdus dicambivorans
Co2+ 1 mM, moderately inhibited Rhizorhabdus dicambivorans
EDTA 5 mM, moderately inhibited Rhizorhabdus dicambivorans
Hg2+ 1 mM, severely inhibited Rhizorhabdus dicambivorans
Mn2+ 1 mM, moderately inhibited Rhizorhabdus dicambivorans
Ni2+ 1 mM, moderately inhibited Rhizorhabdus dicambivorans
Zn2+ 1 mM, severely inhibited Rhizorhabdus dicambivorans

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0181
-
 2,5-Dihydroxybenzoate pH 7.4, 30°C Rhizorhabdus dicambivorans
0.036
-
 3-Chlorogentisate pH 7.4, 30°C Rhizorhabdus dicambivorans

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ 1 mM, enhances activity Rhizorhabdus dicambivorans
Fe3+ 1 mM, enhances activity Rhizorhabdus dicambivorans
Na+ 1 mM, enhances activity Rhizorhabdus dicambivorans

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
70000
-
 gel filtration Rhizorhabdus dicambivorans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2,5-dihydroxybenzoate + O2 Rhizorhabdus dicambivorans
-
 maleylpyruvate
-
 ?
2,5-dihydroxybenzoate + O2 Rhizorhabdus dicambivorans Ndbn-20
-
 maleylpyruvate
-
 ?
3-chlorogentisate + O2 Rhizorhabdus dicambivorans
-
 3-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
 ?
3-chlorogentisate + O2 Rhizorhabdus dicambivorans Ndbn-20
-
 3-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
 ?

Organism

Organism UniProt Comment Textmining
Rhizorhabdus dicambivorans
-
-
-
Rhizorhabdus dicambivorans Ndbn-20
-
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Rhizorhabdus dicambivorans

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
0.6
-
 substrate: 2,5-dihydroxybenzoate, pH 7.4, 30°C Rhizorhabdus dicambivorans
15.4
-
 substrate: 3-chlorogentisate, pH 7.4, 30°C Rhizorhabdus dicambivorans

Storage Stability

Storage Stability Organism
-80°C, 2 weeks, purified enzyme loses 50% of its initial activity. Addition of 2.0 mM GSH (or cysteine), 0.1 mM Fe(NH4)2(SO4)2*6H2O, and 10% glycerol stabilizes the activity Rhizorhabdus dicambivorans

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2,5-dihydroxybenzoate + O2
-
 Rhizorhabdus dicambivorans maleylpyruvate
-
 ?
2,5-dihydroxybenzoate + O2
-
 Rhizorhabdus dicambivorans Ndbn-20 maleylpyruvate
-
 ?
3-chlorogentisate + O2
-
 Rhizorhabdus dicambivorans 3-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
 ?
3-chlorogentisate + O2
-
 Rhizorhabdus dicambivorans Ndbn-20 3-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
 ?
additional information no activity with 3,6-dichlorogentisate or 6-chlorogentisate Rhizorhabdus dicambivorans ?
-
-
additional information no activity with 3,6-dichlorogentisate or 6-chlorogentisate Rhizorhabdus dicambivorans Ndbn-20 ?
-
-

Subunits

Subunits Comment Organism
dimer 2 * 39700, SDS-PAGE Rhizorhabdus dicambivorans

Synonyms

Synonyms Comment Organism
DsmD
-
 Rhizorhabdus dicambivorans

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
 in 50 mM Tris-HCl Rhizorhabdus dicambivorans

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.37
-
 2,5-Dihydroxybenzoate pH 7.4, 30°C Rhizorhabdus dicambivorans
10.33
-
 3-Chlorogentisate pH 7.4, 30°C Rhizorhabdus dicambivorans

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
-
 Rhizorhabdus dicambivorans

Expression

Organism Comment Expression
Rhizorhabdus dicambivorans transcription of dsmD is induced by 3-chlorogentisate but not gentisate up

General Information

General Information Comment Organism
malfunction disruption of dsmD results in a significant decline in the degradation rates of 3-chlorogentisate and the herbicide dicamba but has no effect on the degradation of gentisate. The disruption of both dsmD and gtdA leads to the inability to degrade 3-chlorogentisate and gentisate Rhizorhabdus dicambivorans
physiological function DsmD is specifically responsible for cleavage of 3-chlorogentisate, a key intermediate in the catabolism of the herbicide dicamba in Rhizorhabdus dicambivorans Ndbn-20 Rhizorhabdus dicambivorans

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
20.44
-
 2,5-Dihydroxybenzoate pH 7.4, 30°C Rhizorhabdus dicambivorans
286.1
-
 3-Chlorogentisate pH 7.4, 30°C Rhizorhabdus dicambivorans