Literature summary for 2.7.4.6 extracted from

Lopez-Zavala, A.A.; Quintero-Reyes, I.E.; Carrasco-Miranda, J.S.; Stojanoff, V.; Weichsel, A.; Rudino-Pinera, E.; Sotelo-Mundo, R.R.
Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates (2014), Acta Crystallogr. Sect. F, 70, 1150-1154.

Cloned(Commentary)

Cloned (Comment)	Organism
functional recombinant expression in Escherichia coli	Penaeus vannamei

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme in binary complexes with purine and pyrimidine nucleoside diphosphates, acceptors dADP and dCDP and donor ADP, mixing of 0.001 ml of 20 mg/ml protein in 100 mM NaCl, 40 mM MgCl2, 4mM DTT, and 20 mM nucleotides with 0.001 ml of reservoir solution containing 0.2 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000 or 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000, or 0.2 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5, 30% v/v 2-propanol, 3-7 days, 16°C, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement	Penaeus vannamei

Crystallization (Comment)

Organism

purified recombinant enzyme in binary complexes with purine and pyrimidine nucleoside diphosphates, acceptors dADP and dCDP and donor ADP, mixing of 0.001 ml of 20 mg/ml protein in 100 mM NaCl, 40 mM MgCl2, 4mM DTT, and 20 mM nucleotides with 0.001 ml of reservoir solution containing 0.2 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000 or 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000, or 0.2 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5, 30% v/v 2-propanol, 3-7 days, 16°C, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement

Penaeus vannamei

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Penaeus vannamei

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
57000	-	about, trimeric enzyme in solution	Penaeus vannamei

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + nucleoside diphosphate	Penaeus vannamei	this reaction is a reversible phosphate transfer to both ribonucleoside and deoxyribonucleoside diphosphates using NTP as a phosphate donor to provide adequate nucleosides for RNA or DNA synthesis	ADP + nucleoside triphosphate	-	r

Organism

Organism	UniProt	Comment	Textmining
Penaeus vannamei	A5J299	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant enzyme from Escherichia coli	Penaeus vannamei

Reaction

Reaction	Comment	Organism	Reaction ID
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate	the reaction catalyzed by NDK starts with the transfer of a phosphate from ATP to His117. ADP is then released and the acceptor nucleoside diphosphate is bound and phosphorylated. Nucleotide phosphates are coordinated by a network of basic Arg and His residues, and a polar Thr. All NDKs follow a ping-pong enzymatic mechanism involving a phosphorylated histidine residue in the active site	Penaeus vannamei	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ADP + dADP	-	Penaeus vannamei	AMP + dATP	-	r
ADP + dCDP	low activity	Penaeus vannamei	AMP + dCTP	-	r
ADP + dGDP	-	Penaeus vannamei	AMP + dGTP	-	r
ATP + nucleoside diphosphate	-	Penaeus vannamei	ADP + nucleoside triphosphate	-	r
ATP + nucleoside diphosphate	this reaction is a reversible phosphate transfer to both ribonucleoside and deoxyribonucleoside diphosphates using NTP as a phosphate donor to provide adequate nucleosides for RNA or DNA synthesis	Penaeus vannamei	ADP + nucleoside triphosphate	-	r
additional information	enzyme LvNDK has relaxed substrate specificity and binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with low binding interaction for dCDP. The binding of deoxy- or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 20-hydroxyl group of the ribose moiety. This allows Lys11 to maintain a catalytically favourable conformation independently of the kind of sugar found in the nucleotide	Penaeus vannamei	?	-	?

Subunits

Subunits	Comment	Organism
hexamer	crystal structure analysis	Penaeus vannamei
trimer	in solution	Penaeus vannamei

Synonyms

Synonyms	Comment	Organism
NDK	-	Penaeus vannamei
nucleoside diphosphate kinase	-	Penaeus vannamei

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Penaeus vannamei

Expression

Organism	Comment	Expression
Penaeus vannamei	the NDK enzyme expression is regulated under viral infection	additional information

General Information

General Information	Comment	Organism
additional information	LvNDK has a nucleotide-binding site and a catalytic histidine nucleophile His117, which is part of a phosphorelay that transfers a phosphoryl group obtained from ATP to the nucleoside diphosphate, substrate binding structures, overview	Penaeus vannamei
physiological function	the enzyme catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Enzyme NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism	Penaeus vannamei