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Literature summary for 3.5.4.40 extracted from

  • Goble, A.M.; Toro, R.; Li, X.; Ornelas, A.; Fan, H.; Eswaramoorthy, S.; Patskovsky, Y.; Hillerich, B.; Seidel, R.; Sali, A.; Shoichet, B.K.; Almo, S.C.; Swaminathan, S.; Tanner, M.E.; Raushel, F.M.
    Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes (2013), Biochemistry, 52, 6525-6536.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.5.4.40

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3) cells Deinococcus radiodurans
expressed in Escherichia coli BL21(DE3) cells Streptomyces avermitilis
expressed in Escherichia coli BL21(DE3) cells Nitratiruptor sp. SB155-2
expressed in Escherichia coli Rosetta2 (DE3) cells Acidothermus cellulolyticus

Crystallization (Commentary)

Crystallization (Comment) Organism
sitting drop vapor diffusion method, using 30% (w/v) PEG MME500, 0.1 M Bis-Tris, pH 6.5, and 50 mM calcium chloride Deinococcus radiodurans

Protein Variants

Protein Variants Comment Organism
R87A the mutant shows reduced activity towards 6-amino-6-deoxyfutalosine and adenosine compared to the wild type enzyme Streptomyces avermitilis
R87M the mutant shows reduced activity towards 6-amino-6-deoxyfutalosine and increased activity towards adenosine compared to the wild type enzyme Streptomyces avermitilis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0009
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.0018
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
0.0034
-
 6-amino-6-deoxyfutalosine mutant enzyme R87A, at pH 7.5 and at 30°C Streptomyces avermitilis
0.0048
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.006
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.008
-
 6-amino-6-deoxyfutalosine mutant enzyme R87M, at pH 7.5 and at 30°C Streptomyces avermitilis
0.0083
-
 adenosine mutant enzyme R87A, at pH 7.5 and at 30°C Streptomyces avermitilis
0.01
-
 adenosine mutant enzyme R87M, at pH 7.5 and at 30°C Streptomyces avermitilis
0.037
-
 2'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
0.042
-
 5'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.061
-
 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.094
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.1 1 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ contains Zn2+ Deinococcus radiodurans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6-amino-6-deoxyfutalosine + H2O Acidothermus cellulolyticus
-
 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O Deinococcus radiodurans
-
 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O Streptomyces avermitilis
-
 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O Nitratiruptor sp. SB155-2
-
 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O Acidothermus cellulolyticus 11B
-
 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O Streptomyces avermitilis MA-4680
-
 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539
-
 futalosine + NH3
-
 ?

Organism

Organism UniProt Comment Textmining
Acidothermus cellulolyticus A0LRH8
-
-
Acidothermus cellulolyticus 11B A0LRH8
-
-
Deinococcus radiodurans Q9RW45
-
-
Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539 Q9RW45
-
-
Nitratiruptor sp. SB155-2 A6Q234
-
-
Streptomyces avermitilis Q82K09
-
-
Streptomyces avermitilis MA-4680 Q82K09
-
-

Purification (Commentary)

Purification (Comment) Organism
HisTrap column chromatography and Superdex 200 gel filtration Acidothermus cellulolyticus
HisTrap column chromatography and Superdex 200 gel filtration Deinococcus radiodurans
HisTrap column chromatography and Superdex 200 gel filtration Streptomyces avermitilis
Strep-Tactin column column chromatography, HisTrap column chromatography, and Superdex 200 gel filtration Nitratiruptor sp. SB155-2

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Deinococcus radiodurans ?
-
 ?
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Streptomyces avermitilis ?
-
 ?
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Acidothermus cellulolyticus 11B ?
-
 ?
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Streptomyces avermitilis MA-4680 ?
-
 ?
1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide + H2O
-
 Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539 ?
-
 ?
2'-deoxyadenosine + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
2'-deoxyadenosine + H2O
-
 Deinococcus radiodurans ?
-
 ?
2'-deoxyadenosine + H2O
-
 Streptomyces avermitilis ?
-
 ?
2'-deoxyadenosine + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
3'-deoxyadenosine + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
3'-deoxyadenosine + H2O
-
 Deinococcus radiodurans ?
-
 ?
3'-deoxyadenosine + H2O
-
 Streptomyces avermitilis ?
-
 ?
3'-deoxyadenosine + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
5'-deoxyadenosine + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
5'-deoxyadenosine + H2O
-
 Deinococcus radiodurans ?
-
 ?
5'-deoxyadenosine + H2O
-
 Streptomyces avermitilis ?
-
 ?
5'-deoxyadenosine + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
5'-methylthioadenosine + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
5'-methylthioadenosine + H2O
-
 Deinococcus radiodurans ?
-
 ?
5'-methylthioadenosine + H2O
-
 Streptomyces avermitilis ?
-
 ?
5'-methylthioadenosine + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
5'-methylthioadenosine + H2O
-
 Acidothermus cellulolyticus 11B ?
-
 ?
5'-methylthioadenosine + H2O
-
 Streptomyces avermitilis MA-4680 ?
-
 ?
5'-methylthioadenosine + H2O
-
 Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539 ?
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Acidothermus cellulolyticus futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Deinococcus radiodurans futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Streptomyces avermitilis futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Nitratiruptor sp. SB155-2 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Acidothermus cellulolyticus 11B futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Streptomyces avermitilis MA-4680 futalosine + NH3
-
 ?
6-amino-6-deoxyfutalosine + H2O
-
 Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539 futalosine + NH3
-
 ?
adenosine + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
adenosine + H2O
-
 Deinococcus radiodurans ?
-
 ?
adenosine + H2O
-
 Streptomyces avermitilis ?
-
 ?
adenosine + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
AMP + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
AMP + H2O
-
 Deinococcus radiodurans ?
-
 ?
AMP + H2O
-
 Streptomyces avermitilis ?
-
 ?
AMP + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
AMP + H2O
-
 Acidothermus cellulolyticus 11B ?
-
 ?
AMP + H2O
-
 Streptomyces avermitilis MA-4680 ?
-
 ?
AMP + H2O
-
 Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539 ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Acidothermus cellulolyticus ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Deinococcus radiodurans ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Streptomyces avermitilis ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Nitratiruptor sp. SB155-2 ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Acidothermus cellulolyticus 11B ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Streptomyces avermitilis MA-4680 ?
-
 ?
S-adenosyl-L-homocysteine + H2O
-
 Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539 ?
-
 ?

Synonyms

Synonyms Comment Organism
Acel0264
-
 Acidothermus cellulolyticus
Dr0824
-
 Deinococcus radiodurans
Nis0429
-
 Nitratiruptor sp. SB155-2
Sav2595
-
 Streptomyces avermitilis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.007
-
 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.017
-
 5'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.094
-
 6-amino-6-deoxyfutalosine mutant enzyme R87A, at pH 7.5 and at 30°C Streptomyces avermitilis
0.106
-
 adenosine mutant enzyme R87A, at pH 7.5 and at 30°C Streptomyces avermitilis
0.31
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.4
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.41
-
 adenosine mutant enzyme R87M, at pH 7.5 and at 30°C Streptomyces avermitilis
0.42
-
 6-amino-6-deoxyfutalosine mutant enzyme R87M, at pH 7.5 and at 30°C Streptomyces avermitilis
0.72
-
 2'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
1.2
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
3.8
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
6.8
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
8.6
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.003
-
 AMP wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.005
-
 2'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.006
-
 3'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.011
-
 adenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.02
-
 adenosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.021
-
 AMP wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
0.024
-
 S-adenosyl-L-homocysteine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.024
-
 3'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
0.028
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.032
-
 AMP wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.034
-
 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.044
-
 3'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.045
-
 AMP wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.047
-
 5'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.051
-
 2'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.079
-
 S-adenosyl-L-homocysteine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.11
-
 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
0.11
-
 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
0.24
-
 3'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.31
-
 S-adenosyl-L-homocysteine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
0.41
-
 5'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
1.1
-
 2'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
2.8
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
2.9
-
 5'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
4.3
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
7
-
 S-adenosyl-L-homocysteine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
10
-
 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-beta-D-ribofuranuronamide wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
13
-
 adenosine mutant enzyme R87A, at pH 7.5 and at 30°C Streptomyces avermitilis
18
-
 adenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
19
-
 2'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
22
-
 adenosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
27
-
 6-amino-6-deoxyfutalosine mutant enzyme R87A, at pH 7.5 and at 30°C Streptomyces avermitilis
34
-
 5'-methylthioadenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
41
-
 adenosine mutant enzyme R87M, at pH 7.5 and at 30°C Streptomyces avermitilis
53
-
 6-amino-6-deoxyfutalosine mutant enzyme R87M, at pH 7.5 and at 30°C Streptomyces avermitilis
74
-
 5'-deoxyadenosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans
790
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Streptomyces avermitilis
1100
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Acidothermus cellulolyticus
1300
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Nitratiruptor sp. SB155-2
4800
-
 6-amino-6-deoxyfutalosine wild type enzyme, at pH 7.5 and at 30°C Deinococcus radiodurans