Literature summary for 3.1.3.15 extracted from

Jha, B.; Kumar, D.; Sharma, A.; Dwivedy, A.; Singh, R.; Biswal, B.K.
Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis (2018), J. Biol. Chem., 293, 10102-10118 .

Application

Application	Comment	Organism
drug development	the absence of a histidine biosynthesis pathway in humans, coupled with histidine essentiality for survival of the important human pathogen Mycobacterium tuberculosis (Mtb), underscores the importance of the bacterial enzymes of this pathway as major antituberculosis drug targets	Mycobacterium tuberculosis

Cloned(Commentary)

Cloned (Comment)	Organism
gene hisN or Rv3137, DNA and amino acid sequence analysis, sequence comparisons and phylogenetic analysis, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli and Mycobacterium smegmatis strain mc24517	Mycobacterium tuberculosis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant wild-type enzyme free or in complex with substrate histidinol phosphate, hanging drop vapor diffusion method, mixing of 0.0015 ml of protein solution containing 0.1 mM Zn2+ and 7.5 mM substrate for the complexed crystals, with 0.015 ml of reservoir solution containing 1 M ammonium sulfate, and 750 nl additive which is praseodymium (III) acetate hydrate, 35-40 days, 23°C, X-ray diffraction structure determination and analysis at 1.95 A and 2.90 A, respectively	Mycobacterium tuberculosis

Crystallization (Comment)

Organism

purified recombinant wild-type enzyme free or in complex with substrate histidinol phosphate, hanging drop vapor diffusion method, mixing of 0.0015 ml of protein solution containing 0.1 mM Zn2+ and 7.5 mM substrate for the complexed crystals, with 0.015 ml of reservoir solution containing 1 M ammonium sulfate, and 750 nl additive which is praseodymium (III) acetate hydrate, 35-40 days, 23°C, X-ray diffraction structure determination and analysis at 1.95 A and 2.90 A, respectively

Mycobacterium tuberculosis

Protein Variants

Protein Variants	Comment	Organism
D213A	site-directed mutagenesis	Mycobacterium tuberculosis
D44A	site-directed mutagenesis	Mycobacterium tuberculosis
D83A	site-directed mutagenesis	Mycobacterium tuberculosis
E67A	site-directed mutagenesis	Mycobacterium tuberculosis
T88A	site-directed mutagenesis	Mycobacterium tuberculosis

Inhibitors

Inhibitors	Comment	Organism
3-[(1-(R))-1-(2,6-dichloro-4-fluorophenyl)ethoxy]-5-(1-piperidin-4-ylpyrazol-4-yl)pyridin-2-amine	NSC756645	Mycobacterium tuberculosis
4-chloro-1-N,3-N-bis[4-(4,5-dihydro-1H-imidazol-2-yl)phenyl]benzene-1,3-dicarboxamide	NSC67436	Mycobacterium tuberculosis
5,11-dimethyl-2-(2-piperidin-1-ylethyl)-6H-pyrido[4,3-b]carbazol-2-ium-9-ol	NSC311153, best tested inhibitor	Mycobacterium tuberculosis
additional information	identification of several small-molecule inhibitors of the enzyme by target-based screening against HolPase, high-throughput compound library screening	Mycobacterium tuberculosis
vinorelbine	NSC608210	Mycobacterium tuberculosis
[(1S,4aR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,9,10,10a-hexahydrophenanthren-1-yl]methanamine benzoic acid	NSC65238	Mycobacterium tuberculosis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	Michaelis-Menten kinetics	Mycobacterium tuberculosis
0.03198	-	L-histidinol phosphate	pH 8.0, 37°C, recombinant enzyme	Mycobacterium tuberculosis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	a divalent cation is required, saturation kinetics for Mtb HolPase with Mg2+ as a cofactor, the specificity constant (kcat/Km) with Zn2+ is 1.16fold higher compared to Mg2+, metal binding in the active site of Mtb HolPase, structure, overview	Mycobacterium tuberculosis
Zn2+	a divalent cation is required, saturation kinetics for Mtb HolPase with Zn2+ as a cofactor, the specificity constant (kcat/Km) with Zn2+ is 1.16fold higher compared to Mg2+, Michaelis-Menten kinetics, overview	Mycobacterium tuberculosis

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
56000	-	about, recombinant enzyme, gel filtration	Mycobacterium tuberculosis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
L-histidinol phosphate + H2O	Mycobacterium tuberculosis	-	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	Mycobacterium tuberculosis H37Rv	-	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	Mycobacterium tuberculosis ATCC 25618	-	L-histidinol + phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Mycobacterium tuberculosis	P95189	-	-
Mycobacterium tuberculosis ATCC 25618	P95189	-	-
Mycobacterium tuberculosis H37Rv	P95189	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography and gel filtration	Mycobacterium tuberculosis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
L-histidinol phosphate + H2O	-	Mycobacterium tuberculosis	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate	Mycobacterium tuberculosis	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	-	Mycobacterium tuberculosis H37Rv	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate	Mycobacterium tuberculosis H37Rv	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	-	Mycobacterium tuberculosis ATCC 25618	L-histidinol + phosphate	-	?
L-histidinol phosphate + H2O	the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate	Mycobacterium tuberculosis ATCC 25618	L-histidinol + phosphate	-	?
additional information	no activity with inositol monophosphate by wild-type or mutant Mtb HolPases. Phosphate detection with malachite green	Mycobacterium tuberculosis	?	-	?
additional information	no activity with inositol monophosphate by wild-type or mutant Mtb HolPases. Phosphate detection with malachite green	Mycobacterium tuberculosis H37Rv	?	-	?
additional information	no activity with inositol monophosphate by wild-type or mutant Mtb HolPases. Phosphate detection with malachite green	Mycobacterium tuberculosis ATCC 25618	?	-	?

Subunits

Subunits	Comment	Organism
dimer	2 * 28620, recombinant enzyme, SDS-PAGE	Mycobacterium tuberculosis
More	the dimer is stabilized largely by hydrogen bonds, salt bridges, and van der Waals interactions. Asp189, Val149, Arg183, Asp202, Ala119, Arg171, Asn90, Arg93, Ile31, Arg122, and Ala186 of one monomer form hydrogen-bonding interactions with Arg185, Ile31, Asn90, Arg93, Arg122, Asp179, Tyr187, Gly199, Ser148, Gln121, and Ala186, respectively, of the other monomer and vice versa. There are two catalytic sites in the dimer, but only one product-exit channel shared by the two monomers at the dimer interface	Mycobacterium tuberculosis

Synonyms

Synonyms	Comment	Organism
hisN	-	Mycobacterium tuberculosis
histidinol phosphate phosphatase	-	Mycobacterium tuberculosis
HolPase	-	Mycobacterium tuberculosis
Mtb HolPase	-	Mycobacterium tuberculosis
Rv3137	-	Mycobacterium tuberculosis

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	recombinant enzyme	Mycobacterium tuberculosis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.99	-	L-histidinol phosphate	pH 8.0, 37°C, recombinant enzyme	Mycobacterium tuberculosis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	recombinant enzyme	Mycobacterium tuberculosis

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.09425	-	pH 8.0, 37°C, recombinant enzyme	Mycobacterium tuberculosis	5,11-dimethyl-2-(2-piperidin-1-ylethyl)-6H-pyrido[4,3-b]carbazol-2-ium-9-ol

General Information

General Information	Comment	Organism
evolution	enzyme Mtb HolPase belongs to the IMPase family, it is not an active inositol monophosphate phosphatase (IMPase) but a histidinol phosphate phosphatase (HolPase)	Mycobacterium tuberculosis
additional information	the cocrystal structure of Mtb HolPase with HOLP reveals a unique mode of substrate binding, a multizinc active-site pocket, and a product-exit channel. Dephosphorylation mechanism of Mtb Hol-Pase, overview	Mycobacterium tuberculosis
physiological function	the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate	Mycobacterium tuberculosis

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
30.96	-	L-histidinol phosphate	pH 8.0, 37°C, recombinant enzyme	Mycobacterium tuberculosis