Literature summary for 2.7.1.35 extracted from

Are, S.; Gatreddi, S.; Jakkula, P.; Qureshi, I.A.
Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani (2020), Int. J. Biol. Macromol., 152, 812-827 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene pdxK, sequence comparisons, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Codon Plus RIL	Leishmania donovani

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant His-tagged enzyme in complex with ADP, and subsstrate pyridoxamine or pyridoxine or ginkgotoxin, mixing of 0.0015 ml of protein solution containing 6.5 mg/ml protein, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 2 mM ADP, and 2 mM ligand, with reservoir solution containing 0.1 M sodium cacodylate, pH 6.0, 0.32 M calcium acetate, 4% glycerol, and 18% PEG 8000, and equilibration against 0.5 ml reservoir, 22°C, 2 days, X-ray diffraction structure determination and analysis at 1.85-2.0 A resolution, molecular replacement. Method optimization, overview. The apoform of the enzyme does not crystallize	Leishmania donovani

Crystallization (Comment)

Organism

purified recombinant His-tagged enzyme in complex with ADP, and subsstrate pyridoxamine or pyridoxine or ginkgotoxin, mixing of 0.0015 ml of protein solution containing 6.5 mg/ml protein, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 2 mM ADP, and 2 mM ligand, with reservoir solution containing 0.1 M sodium cacodylate, pH 6.0, 0.32 M calcium acetate, 4% glycerol, and 18% PEG 8000, and equilibration against 0.5 ml reservoir, 22°C, 2 days, X-ray diffraction structure determination and analysis at 1.85-2.0 A resolution, molecular replacement. Method optimization, overview. The apoform of the enzyme does not crystallize

Leishmania donovani

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.0297	-	ginkgotoxin	recombinant enzyme, pH 7.5, 37°C	Leishmania donovani
0.0909	-	pyridoxal	recombinant enzyme, pH 7.5, 37°C	Leishmania donovani
0.1818	-	pyridoxamine	recombinant enzyme, pH 7.5, 37°C	Leishmania donovani
0.4347	-	pyridoxine	recombinant enzyme, pH 7.5, 37°C	Leishmania donovani

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required, bindings structure analysis, overview	Leishmania donovani

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
ATP + pyridoxal	Leishmania donovani	-	ADP + pyridoxal 5'-phosphate	-	?
ATP + pyridoxal	Leishmania donovani MHOM/80/IN/Dd8	-	ADP + pyridoxal 5'-phosphate	-	?
ATP + pyridoxamine	Leishmania donovani	-	ADP + pyridoxamine 5'-phosphate	-	?
ATP + pyridoxamine	Leishmania donovani MHOM/80/IN/Dd8	-	ADP + pyridoxamine 5'-phosphate	-	?
ATP + pyridoxine	Leishmania donovani	-	ADP + pyridoxine 5'-phosphate	-	?
ATP + pyridoxine	Leishmania donovani MHOM/80/IN/Dd8	-	ADP + pyridoxine 5'-phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Leishmania donovani	A0A0G2YFI9	-	-
Leishmania donovani MHOM/80/IN/Dd8	A0A0G2YFI9	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) Codon Plus RIL by nickel affinity chromatography and gel filtration	Leishmania donovani

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ATP + ginkgotoxin	ginkgotoxin (from leaves of Ginkgo biloba) acts as pseudo-substrate for pyridoxal kinase with a Km value of 0.0297 mM	Leishmania donovani	?	-	?
ATP + ginkgotoxin	ginkgotoxin (from leaves of Ginkgo biloba) acts as pseudo-substrate for pyridoxal kinase with a Km value of 0.0297 mM	Leishmania donovani MHOM/80/IN/Dd8	?	-	?
ATP + pyridoxal	-	Leishmania donovani	ADP + pyridoxal 5'-phosphate	-	?
ATP + pyridoxal	-	Leishmania donovani MHOM/80/IN/Dd8	ADP + pyridoxal 5'-phosphate	-	?
ATP + pyridoxamine	-	Leishmania donovani	ADP + pyridoxamine 5'-phosphate	-	?
ATP + pyridoxamine	-	Leishmania donovani MHOM/80/IN/Dd8	ADP + pyridoxamine 5'-phosphate	-	?
ATP + pyridoxine	-	Leishmania donovani	ADP + pyridoxine 5'-phosphate	-	?
ATP + pyridoxine	-	Leishmania donovani MHOM/80/IN/Dd8	ADP + pyridoxine 5'-phosphate	-	?

Subunits

Subunits	Comment	Organism
homodimer	2 * 35150, recombinant His-tagged enzyme, SDS-PAGE	Leishmania donovani

Synonyms

Synonyms	Comment	Organism
LdPdxK	-	Leishmania donovani
PdxK	-	Leishmania donovani

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Leishmania donovani

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	recombinant enzyme	Leishmania donovani

pH Range

pH Minimum	pH Maximum	Comment	Organism
4.5	9.5	activity range, recombinant enzyme	Leishmania donovani

General Information

General Information	Comment	Organism
evolution	PdxK belongs to ribokinase enzyme family in which either cysteine or aspartate act as catalytic residue for its activity. The known catalytic mechanism of ribokinase family and for PdxK is the in line displacement mechanism in which hydroxyl group of the substrate is activated by a catalytic base (aspartate) of the enzyme, to make the nucleophilic attack on the gamma-phosphate group of ATP. The active site residues Leu43, Ser47, Ile52, Arg56, Asn87 and Thr227 present in LdPdxK are replaced with Phe43, Thr47, Try52, Val56, Arg86 and Val231 in mammalian PdxKs	Leishmania donovani
additional information	analysis of the binding structures of substrates and products from PdxK-ligand crystal structures, overview	Leishmania donovani
physiological function	the enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal 5'-phosphate (PLP) using ATP as the cosubstrate. The product PLP plays a key role in several biological processes such as transamination, decarboxylation and deamination	Leishmania donovani