Literature summary for 2.7.1.169 extracted from

Kita, A.; Kishimoto, A.; Shimosaka, T.; Tomita, H.; Yokooji, Y.; Imanaka, T.; Atomi, H.; Miki, K.
Crystal structure of pantoate kinase from Thermococcus kodakarensis (2020), Proteins, 88, 718-724 .

Search for more literature for 2.7.1.169

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme in apoform or in complex with ATP and a magnesium ion, mixing of 5-10 mg/ml protein in 50 mM Tris-HCl, pH 7.5, with 18%-20% PEG 8000 solutions containing 200 mM calcium acetate and 100 mM MES, pH 6.0, as a precipitant, 1-2 weeks, 20°C, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, single isomorphous replacement (SIR) method using derivative data of K2Pt (NO2)4 collected at 3.0 A resolution, modeling. In TkPoK/ATP, the adenine ring of the ATP is not included in the crystal structure, because its electron density is very poor	Thermococcus kodakarensis

Crystallization (Comment)

Organism

purified recombinant enzyme in apoform or in complex with ATP and a magnesium ion, mixing of 5-10 mg/ml protein in 50 mM Tris-HCl, pH 7.5, with 18%-20% PEG 8000 solutions containing 200 mM calcium acetate and 100 mM MES, pH 6.0, as a precipitant, 1-2 weeks, 20°C, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, single isomorphous replacement (SIR) method using derivative data of K2Pt (NO2)4 collected at 3.0 A resolution, modeling. In TkPoK/ATP, the adenine ring of the ATP is not included in the crystal structure, because its electron density is very poor

Thermococcus kodakarensis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Thermococcus kodakarensis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
ATP + (R)-pantoate	Thermococcus kodakarensis	-	ADP + (R)-4-phosphopantoate	-	?
ATP + (R)-pantoate	Thermococcus kodakarensis JCM 12380	-	ADP + (R)-4-phosphopantoate	-	?
ATP + (R)-pantoate	Thermococcus kodakarensis ATCC BAA-918	-	ADP + (R)-4-phosphopantoate	-	?

Organism

Organism	UniProt	Comment	Textmining
Thermococcus kodakarensis	Q5JHF1	Pyrococcus kodakaraensis strain KOD1	-
Thermococcus kodakarensis ATCC BAA-918	Q5JHF1	Pyrococcus kodakaraensis strain KOD1	-
Thermococcus kodakarensis JCM 12380	Q5JHF1	Pyrococcus kodakaraensis strain KOD1	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ATP + (R)-pantoate	-	Thermococcus kodakarensis	ADP + (R)-4-phosphopantoate	-	?
ATP + (R)-pantoate	-	Thermococcus kodakarensis JCM 12380	ADP + (R)-4-phosphopantoate	-	?
ATP + (R)-pantoate	-	Thermococcus kodakarensis ATCC BAA-918	ADP + (R)-4-phosphopantoate	-	?
additional information	the enzyme shows broad nucleotide specificity	Thermococcus kodakarensis	?	-	-
additional information	the enzyme shows broad nucleotide specificity	Thermococcus kodakarensis JCM 12380	?	-	-
additional information	the enzyme shows broad nucleotide specificity	Thermococcus kodakarensis ATCC BAA-918	?	-	-

Subunits

Subunits	Comment	Organism
dimer	2 * 33000, about, sequence calculation and crystal structure analysis	Thermococcus kodakarensis

Synonyms

Synonyms	Comment	Organism
PoK	-	Thermococcus kodakarensis
TK2141	-	Thermococcus kodakarensis
TkPoK	-	Thermococcus kodakarensis

Cofactor

Cofactor	Comment	Organism	Structure
ATP	the electron density for the adenosine moiety of ATP is very weak, which most likely relates to its broad nucleotide specificity. The triphosphate moiety of ATP is surrounded by the lycine-rich loop of motif II (P96NGYGFGNSAG106). The magnesium ion can interact with oxygen atoms of beta- and gamma-phosphates, and with the O5' atom of ATP which bridges the adenosine and the triphosphate groups	Thermococcus kodakarensis

General Information

General Information	Comment	Organism
metabolism	the CoA biosynthesis pathway involves reactions that convert pantoate to 4'-phosphopantothenate. For this conversion, bacteria/eukaryotes commonly use two enzymes, pantothenate synthetase (PS) and pantothenate kinase (PanK). In the PS/PanK pathway, pantoate and beta-alanine are first condensed to form pantothenate by the reaction of PS, and then pantothenate is phosphorylated to generate 40-phosphopantothenate by the reaction of PanK	Thermococcus kodakarensis