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Literature summary for 3.2.1.143 extracted from

  • Cho, C.C.; Chien, C.Y.; Chiu, Y.C.; Lin, M.H.; Hsu, C.H.
    Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans (2019), Nat. Commun., 10, 1491 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of wild-type and mutant enzymes Deinococcus radiodurans

Crystallization (Commentary)

Crystallization (Comment) Organism
crystallization of ADP-ribose bound wild-type enzyme and mutant enzymes T267K and T267R, X-ray diffraction structure determination and analysis at 1.97 A resolution, monoclinic crystals with space group P21 Deinococcus radiodurans

Protein Variants

Protein Variants Comment Organism
E112A site-directed mutagenesis, inactive mutant Deinococcus radiodurans
additional information disruption of DrPARG expression causes accumulation of endogenous poly-ADP-ribose (PAR) and compromises recovery from UV radiation damage. A substitution of Arg268 for the smaller and uncharged side chain of Thr267 than that of arginine disrupts the interaction matrix of Thr267, Asp260, and n ribose' and allows for accommodating the n+1 ADP-ribose Deinococcus radiodurans
T267K site-directed mutagenesis, the mutant loses its endoglycohydrolase activity but retains the exo activity on poly(ADP-ribose), PAR Deinococcus radiodurans
T267R site-directed mutagenesis, the mutant loses its endoglycohydrolase activity but retains the exo activity on poly(ADP-ribose), PAR Deinococcus radiodurans

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information Michaelis-Menten kinetics Deinococcus radiodurans
0.00296
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant wild-type enzyme Deinococcus radiodurans
0.00934
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant mutant T267R Deinococcus radiodurans
0.01114
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant mutant T267K Deinococcus radiodurans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
poly(ADP-ribose) + H2O Deinococcus radiodurans
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans R1
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans DSM 20539
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans VKM B-1422
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans NCIMB 9279
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans JCM 16871
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans LMG 4051
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans ATCC 13939
-
?
-
?
poly(ADP-ribose) + H2O Deinococcus radiodurans NBRC 15346
-
?
-
?

Organism

Organism UniProt Comment Textmining
Deinococcus radiodurans Q9RZM4
-
-
Deinococcus radiodurans ATCC 13939 Q9RZM4
-
-
Deinococcus radiodurans DSM 20539 Q9RZM4
-
-
Deinococcus radiodurans JCM 16871 Q9RZM4
-
-
Deinococcus radiodurans LMG 4051 Q9RZM4
-
-
Deinococcus radiodurans NBRC 15346 Q9RZM4
-
-
Deinococcus radiodurans NCIMB 9279 Q9RZM4
-
-
Deinococcus radiodurans R1 Q9RZM4
-
-
Deinococcus radiodurans VKM B-1422 Q9RZM4
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant wild-type and mutant enzymes Deinococcus radiodurans

Reaction

Reaction Comment Organism Reaction ID
(ADP-ribose)n + H2O = (ADP-ribose)n-1 + ADP-ribose enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans R1 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans DSM 20539 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans VKM B-1422 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans NCIMB 9279 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans JCM 16871 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans LMG 4051 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans ATCC 13939 ?
-
?
additional information enzyme DrPARG possesses endoglycohydrolase activity toward poly-ADP-ribose (PAR). DrPARG acts in both exo- and endo-glycohydrolase modes Deinococcus radiodurans NBRC 15346 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans R1 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans R1 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans DSM 20539 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans DSM 20539 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans VKM B-1422 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans VKM B-1422 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans NCIMB 9279 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans NCIMB 9279 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans JCM 16871 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans JCM 16871 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans LMG 4051 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans LMG 4051 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans ATCC 13939 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans ATCC 13939 ?
-
?
poly(ADP-ribose) + H2O
-
Deinococcus radiodurans NBRC 15346 ?
-
?
poly(ADP-ribose) + H2O enzyme-substrate binding complex structure analysis, overview Deinococcus radiodurans NBRC 15346 ?
-
?

Synonyms

Synonyms Comment Organism
DrPARG
-
Deinococcus radiodurans
PARG
-
Deinococcus radiodurans
poly(ADP-ribose)glycohydrolase
-
Deinococcus radiodurans

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Deinococcus radiodurans

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
181.4
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant mutant T267K Deinococcus radiodurans
198.6
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant mutant T267R Deinococcus radiodurans
266.4
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant wild-type enzyme Deinococcus radiodurans

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Deinococcus radiodurans

Expression

Organism Comment Expression
Deinococcus radiodurans in the radio-resistant bacterium Deinococcus radiodurans, the PARG homologue, DrPARG, expression is upregulated after radiation damage up

General Information

General Information Comment Organism
malfunction disruption of DrPARG expression causes accumulation of endogenous poly-ADP-ribose (PAR) and compromises recovery from UV radiation damage. Endogenous PAR levels in Deinococcus radiodurans are elevated after UV irradiation, indicating that the prokaryotic PARylation may be involved in resistance to genotoxic stresses Deinococcus radiodurans
additional information CD spectra of enzyme DrPARG in the absence and presence of ADP-ribose exhibit increased proportion of alpha-helices and beta-strands from 11.78% and 30.37% to 15.10% and 33.52%, respectively, which suggests that conformational changes occur during the binding of ADP-ribose. The intrinsically disordered N-terminal region of DrPARG might be highly flexible. ADP-ribose binding pocket and complex structure, and conformational effects, detailed overview Deinococcus radiodurans

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
16284
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant mutant T267K Deinococcus radiodurans
21263
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant mutant T267R Deinococcus radiodurans
90000
-
Poly(ADP-ribose) pH 7.5, 37°C, recombinant wild-type enzyme Deinococcus radiodurans