Literature summary for 2.7.4.6 extracted from

Hu, Y.; Feng, F.; Liu, Y.
Structural and functional characterization of Acinetobacter baumannii nucleoside diphosphate kinase (2015), Prog. Biochem. Biophys., 42, 260-267.

No PubMed abstract available

Application

Application	Comment	Organism
drug development	the enzyme is a potential target to develop therapeutic approaches to overcome multiresistance of the bacterium against antibiotics	Acinetobacter baumannii

Cloned(Commentary)

Cloned (Comment)	Organism
gene ndk, recombinant expression of tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Acinetobacter baumannii

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant tagged wild-type and mutant enzymes, hanging-drop vapor diffusion method, mixing of 0.001 ml of spontanously degraded 200 mg/ml protein in 50 mmol/L Tris, pH 8.0, 150 mmol/l NaCl, and 5 mmol/l MgCl2, with 0.001 ml of reservoir solution containing 0.1 mol/l potassium sodium tartrate tetrahydrate, and 18% w/v PEG 3350 for the wild-type enzyme and 1 mol/l sodium malonate, pH 7.0, 0.1 mol/l HEPES, pH 7.0, and 0.5% v/v Jeffamine ED-2001, pH 7.0 for the truncated mutant enzymes, X-ray diffraction structure determination and analysis, molecular replacement method using Burkholderia thailandensis NDK, PDB ID 4DUT, as starting model	Acinetobacter baumannii

Crystallization (Comment)

Organism

purified recombinant tagged wild-type and mutant enzymes, hanging-drop vapor diffusion method, mixing of 0.001 ml of spontanously degraded 200 mg/ml protein in 50 mmol/L Tris, pH 8.0, 150 mmol/l NaCl, and 5 mmol/l MgCl2, with 0.001 ml of reservoir solution containing 0.1 mol/l potassium sodium tartrate tetrahydrate, and 18% w/v PEG 3350 for the wild-type enzyme and 1 mol/l sodium malonate, pH 7.0, 0.1 mol/l HEPES, pH 7.0, and 0.5% v/v Jeffamine ED-2001, pH 7.0 for the truncated mutant enzymes, X-ray diffraction structure determination and analysis, molecular replacement method using Burkholderia thailandensis NDK, PDB ID 4DUT, as starting model

Acinetobacter baumannii

Protein Variants

Protein Variants	Comment	Organism
E28A	site-directed mutagenesis the mutation interrupts the secondary structure of the protein leading to declined enzymatic activity compared to wild-type	Acinetobacter baumannii
additional information	construction of a C-terminally truncated mutant, truncation of the C-terminal arginine-threonine-arginine (RTR) residues leads to the instability of the tertiary structure resulting in reduced kinase activity compared to wild-type, mutant crystal structure analysis	Acinetobacter baumannii

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Acinetobacter baumannii

Organism

Organism	UniProt	Comment	Textmining
Acinetobacter baumannii	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by affinity chromatography and gel filtration	Acinetobacter baumannii

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
GTP + ADP	-	Acinetobacter baumannii	GDP + ATP	-	?
additional information	the enzyme catalyzes transfer of the gamma-phosphate from a nucleoside triphosphate (NTP) to a nucleoside diphosphate (NDP)	Acinetobacter baumannii	?	-	?

Subunits

Subunits	Comment	Organism
dimer	Lys33 is a key residue for maintaining dimer interaction when RTR residues are truncated but is not sufficient to keep efficient enzymatic reaction of the C-terminally truncated mutant enzyme	Acinetobacter baumannii

Synonyms

Synonyms	Comment	Organism
NDK	-	Acinetobacter baumannii
nucleoside diphosphate kinase	-	Acinetobacter baumannii

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
22	-	assay at room temperature	Acinetobacter baumannii

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	assay at	Acinetobacter baumannii

General Information

General Information	Comment	Organism
additional information	Acinetobacter baumannii NDK structure comparison with the structure of the Myxococcus xanthus enzyme NDK. Acinetobacter baumannii NDK might share a similar catalytic mechanism with Myxococcus xanthus NDK	Acinetobacter baumannii