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Literature summary for 2.7.4.6 extracted from

  • Kihara, A.; Saburi, W.; Wakuta, S.; Kim, M.H.; Hamada, S.; Ito, H.; Imai, R.; Matsui, H.
    Physiological and biochemical characterization of three nucleoside diphosphate kinase isozymes from rice (Oryza sativa L.) (2011), Biosci. Biotechnol. Biochem., 75, 1740-1745.
    View publication on PubMed
Search for more literature for 2.7.4.6

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3)pLyS cells Oryza sativa

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.079
-
 ADP isozyme NDPK2, with TTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.108
-
 ADP isozyme NDPK3, with TTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.125
-
 ADP isozyme NDPK3, with GTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.138
-
 ADP isozyme NDPK2, with GTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.392
-
 ADP isozyme NDPK1, with TTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.45
-
 GTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.51
-
 GTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.552
-
 ADP isozyme NDPK1, with CTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.578
-
 ADP isozyme NDPK3, with CTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.707
-
 ADP isozyme NDPK1, with GTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
0.89
-
 TTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
1.26
-
 ADP isozyme NDPK2, with CTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
1.34
-
 TTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
1.69
-
 GTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
5.28
-
 TTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
5.28
-
 CTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
6.72
-
 CTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
9.37
-
 CTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa

Localization

Localization Comment Organism GeneOntology No. Textmining
cytosol isozyme NDPK1 Oryza sativa 5829
-
mitochondrion isozyme NDPK3 Oryza sativa 5739
-
plastid isozyme NDPK2 Oryza sativa 9536
-

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
17400
-
 x * 17400, isozyme NDPK2, calculated from amino acid sequence Oryza sativa
17900
-
 x * 17900, isozyme NDPK1, calculated from amino acid sequence Oryza sativa
18000
-
 x * 18000, isozyme NDPK3, calculated from amino acid sequence Oryza sativa

Organism

Organism UniProt Comment Textmining
Oryza sativa
-
 cultivar Kitaake
-

Purification (Commentary)

Purification (Comment) Organism
Ni-chelating Sepharose column chromatography Oryza sativa

Source Tissue

Source Tissue Comment Organism Textmining
leaf
-
 Oryza sativa
-
leaf sheath
-
 Oryza sativa
-
additional information isoform NDPK1 is weakly expressed in leaf sheaths Oryza sativa
-
seed immature seed Oryza sativa
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ADP + CTP
-
 Oryza sativa ATP + CDP
-
 ?
ADP + GTP
-
 Oryza sativa ATP + GDP
-
 ?
ADP + TTP
-
 Oryza sativa ATP + TDP
-
 ?

Subunits

Subunits Comment Organism
? x * 17400, isozyme NDPK2, calculated from amino acid sequence Oryza sativa
? x * 17900, isozyme NDPK1, calculated from amino acid sequence Oryza sativa
? x * 18000, isozyme NDPK3, calculated from amino acid sequence Oryza sativa

Synonyms

Synonyms Comment Organism
NDPK1 isozyme Oryza sativa
NDPK2 isozyme Oryza sativa
NDPK3 isozyme Oryza sativa
nucleoside diphosphate kinase
-
 Oryza sativa

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
40 60 after 15 min incubation at 40°C, isozymes NDPK1 and NDPK3 show about 40% and 80% residual activity and no activity at 60°C, respectively, while isozyme NDPK2 shows about 40% residual activity at 60°C Oryza sativa

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
14.2
-
 TTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
17.9
-
 GTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
27.7
-
 GTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
33.5
-
 TTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
49.4
-
 GTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
55
-
 TTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
85.2
-
 CTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
89
-
 CTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
229
-
 CTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
6.2
-
 isozymes NDPK2 and NDPK3 Oryza sativa
8.4
-
 isozyme NDPK1 Oryza sativa

pH Stability

pH Stability pH Stability Maximum Comment Organism
4 9 isozyme NDPK3 Oryza sativa
6 9 isozyme NDPK2 Oryza sativa
7 9 isozyme NDPK1 Oryza sativa

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
9.1
-
 CTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
10.4
-
 TTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
16
-
 TTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
16.9
-
 CTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
25
-
 TTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
29.2
-
 GTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
34.1
-
 CTP isozyme NDPK1, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
35.1
-
 GTP isozyme NDPK3, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
61.6
-
 GTP isozyme NDPK2, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
67.6
-
 ADP isozyme NDPK2, with CTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
69.9
-
 ADP isozyme NDPK1, with GTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
140
-
 ADP isozyme NDPK1, with TTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
143
-
 ADP isozyme NDPK3, with GTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
154
-
 ADP isozyme NDPK3, with CTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
180
-
 ADP isozyme NDPK2, with TTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
210
-
 ADP isozyme NDPK2, with GTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
310
-
 ADP isozyme NDPK3, with TTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa
415
-
 ADP isozyme NDPK1, with CTP as cosubstrate, in 4 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, at 25°C Oryza sativa