Literature summary for 3.1.3.5 extracted from

Wallden, K.; Nordlund, P.
Structural basis for the allosteric regulation and substrate recognition of human cytosolic 5-nucleotidase II (2011), J. Mol. Biol., 408, 684-696.

Activating Compound

Activating Compound	Comment	Organism
2,3-bisphosphoglycerate	allosteric activation	Homo sapiens
ATP	allosteric activation	Homo sapiens
diadenosine polyphosphate	allosteric activation	Homo sapiens
additional information	structural basis for the allosteric activation of cN-II via a mechanism where an effector-induced disorder-to-order transition generates rearrangements within the catalytic site and the subsequent coordination of the catalytically essential magnesium. Central to the activation is the large transition of the catalytically essential Asp356. Neither substrate nor Mg2+ bound to this form, supporting an allosteric mechanism in which effector-induced conformational changes are required to increase the affinity for Mg2+ and the substrate	Homo sapiens

Cloned(Commentary)

Cloned (Comment)	Organism
expression of mutant D52N in Escherichia coli strain BL21(DE)-R3-pRARE2	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
analysis of crystal structures of the inactive D52N mutant enzyme in apoform or in complexes with 1. 2,3-bisphosphoglycerate, 2. IMP/ATP, 3. IMP/2,3-bisphosphoglycerate, 4. GMP/diadenosine tetraphosphate, 5. dGMP/dATP, or 6. UMP/ATP, overview. Crystallization by sitting drop vapor diffusion method with sitting drops of 300 nl at a protein solution/reservoir solution ratio of 2:1, the reservoir solution contains 0.1 M bicine, pH 9.0, and 10% w/v PEG 6000, with 20 mM MgCl2, 10 mM dATP, and 10 mM dGMP added to the protein solution, 7.7 mg/ml protein, 1-2 weeks at 4°C, to obtain the enzyme complexes the crystals are soaked in 0.01 ml drops of reservoir solution supplemented with 10 mM of the corresponding substrate/activator and 20 mM MgCl2 for 90 min, X-ray diffraction structure determination and analysis at A resolution	Homo sapiens

Crystallization (Comment)

Organism

analysis of crystal structures of the inactive D52N mutant enzyme in apoform or in complexes with 1. 2,3-bisphosphoglycerate, 2. IMP/ATP, 3. IMP/2,3-bisphosphoglycerate, 4. GMP/diadenosine tetraphosphate, 5. dGMP/dATP, or 6. UMP/ATP, overview. Crystallization by sitting drop vapor diffusion method with sitting drops of 300 nl at a protein solution/reservoir solution ratio of 2:1, the reservoir solution contains 0.1 M bicine, pH 9.0, and 10% w/v PEG 6000, with 20 mM MgCl2, 10 mM dATP, and 10 mM dGMP added to the protein solution, 7.7 mg/ml protein, 1-2 weeks at 4°C, to obtain the enzyme complexes the crystals are soaked in 0.01 ml drops of reservoir solution supplemented with 10 mM of the corresponding substrate/activator and 20 mM MgCl2 for 90 min, X-ray diffraction structure determination and analysis at A resolution

Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
D52N	site-directed mutagenesis, catalytically inactive active site residue	Homo sapiens

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
cytosol	-	Homo sapiens	5829	-

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required, catalytically essential	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
additional information	Homo sapiens	cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	P49902	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
5'-AMP + H2O	-	Homo sapiens	adenosine + phosphate	-	?
5'-dGMP + H2O	-	Homo sapiens	deoxyguanosine + phosphate	-	?
5'-GMP + H2O	-	Homo sapiens	guanosine + phosphate	-	?
5'-IMP + H2O	-	Homo sapiens	inosine + phosphate	-	?
5'-UMP + H2O	-	Homo sapiens	uridine + phosphate	-	?
additional information	cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates	Homo sapiens	?	-	?
additional information	structural basis for the substrate specificity of cN-II: Arg202, Asp206, and Phe157 seem to be important residues for purine/pyrimidine selectivity	Homo sapiens	?	-	?

Subunits

Subunits	Comment	Organism
More	cN-II is a relatively large enzyme of the structural HAD superfamily, which contains, besides the alpha/beta-Rossmann fold and the four-helix bundle, non-conserved regions involved in effector binding and subunit-subunit interactions	Homo sapiens
tetramer	cN-II functions as a tetramer forming a dimer of dimers, structural basis for the allosteric regulation and substrate recognition of cytosolic 5-nucleotidase II, overview. The effector binding site, corresponding to effector site 1, is located close to one of the subunit interfaces where the effector takes part in subunit-subunit interactions by forming electrostatic interactions between the effector phosphates and the positively charged residues of each subunit	Homo sapiens

Synonyms

Synonyms	Comment	Organism
cN-II	-	Homo sapiens
cytosolic 5'-nucleotidase II	-	Homo sapiens
More	cN-II is a relatively large enzyme of the structural HAD superfamily	Homo sapiens

General Information

General Information	Comment	Organism
metabolism	the nucleotide salvage pathway is regulated at a molecular level	Homo sapiens
additional information	the enzyme interferes with the phosphorylation-dependent activation of nucleoside analogues used in the treatment of cancer and viral diseases	Homo sapiens
physiological function	cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and participates in the regulation of purine nucleotide pools within the cell	Homo sapiens