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3.1.3.5: 5'-nucleotidase

This is an abbreviated version!
For detailed information about 5'-nucleotidase, go to the full flat file.

Word Map on EC 3.1.3.5

Reaction

A 5'-ribonucleotide
+
H2O
=
a ribonucleoside
 +
phosphate

Synonyms

5'-adenylic phosphatase, 5'-AMP nucleotidase, 5'-AMPase, 5'-ectonucleotidase, 5'-mononucleotidase, 5'-NT, 5'-NT-1, 5'-NT-2, 5'-NT-3, 5'-NT-4, 5'-nucleotidase, 5'-nucleotidase A, 5'-nucleotidase I, 5'-nucleotidase II, 5'Nase, 5'nucleotidase, 5nA, 5NT, adenosine 5'-monophosphatase, adenosine 5'-phosphatase, adenosine monophosphatase, AMP phosphatase, AMP phosphohydrolase, AMP-selective 5'-nucleotidase, AMPase, c-N-I, c-N-II, Cant1, CD73, CD73 antigen, CD73/ecto-5'-nucleotidase, class C acid phosphatase, cN-I, cN-IA, cN-II, cN-III, cNI, cNII, cNIIIB nucleotidase, cytoplasmic 5'-nucleotidase II, cytoplasmic 5'-nucleotidase II (IMP-selective or GMP/IMP-selective), cytoplasmic 5'-nucleotidase III, cytoplasmic 5'-nucleotidase-I (AMP-selective), cytosolic 5'-nucleotidase, cytosolic 5'-nucleotidase II, cytosolic 5'-nucleotidase/phosphotransferase, E-5'-Nu, e-5NT, e-N, e5'-NT, e5'NT, ecto 5'-NT, ecto 5'-nucleotidase, ecto-5' nucleotidase, ecto-5'-NT, ecto-5'-NT/CD73, ecto-5'-nucleotidase, ecto-5'-nucleotidase/CD73, ecto-5'nucleotidase, ecto-5-NT, ecto-5-nucleotidase, ecto-nucleotidase, ectonuceotidase, ectonucleotidase, ectonucleotidase CD73, eN, eNs, eNT, GA-AMPase, high Km 5'-nucleotidase, high-Km 5'-NT, hppA gene product, IMP 5'-nucleotidase, IMP-GMP 5'-nucleotidase, IMP-GMP specific nucleotidase, IMP-specific, high Km 5'-nucleotidase, IMP/GMP selective 5'-NT, Isn1, membrane-bound 5'-nucleotidase, More, NMN 5'-nucleotidase, NT5C3A, NT5E, P5'N-1, Phm8, Pho5, PM-AMPase, PN-1, PN-I, purine 5'-NT, purine 5'-nucleotidase, pyrimidine 5'-nucleotidase, Sdt1, snake venom 5'-nucleotidase, soluble calcium-activated nucleotidase 1, thymidine monophosphate nucleotidase, type II cytosolic 5'-nucleotidase, UMPase, UMPH-1, uridine 5'-nucleotidase, uridine monophosphate hydrolase-1, UshA, XF_2089, YutF

ECTree

     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.3 Phosphoric-monoester hydrolases
                3.1.3.5 5'-nucleotidase

Crystallization

Crystallization on EC 3.1.3.5 - 5'-nucleotidase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
four different crystal forms: analysis of the structure of ATP bound to the enzyme in crystal form I, which contains one molecule in the asymmetric unit, the structure of an enzyme/adenosine/phosphate complex in crystal form III, which contains two independent molecules and the structure of alpha,beta-methylene-ADP in complex with the enzyme in crystal form IV, containing four complexes in the asymmetric unit
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
in complex with adenosine, inhibitors 2,2'-(2-(2-((2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-carboxamido)ethylamino)-2-oxoethylazanediyl) diacetic acid, baicalin and ADP analog AMPCP. The dimeric enzyme undergoes an extensive 114° conformational switch between the open and closed forms. The dimerization interface is formed by the C-terminal domains and exhibits interchain motions of up to 13°. Structural control of the domain movement determines the selectivity for monophosphate nucleotides
molecular modeling study using inhibitor 1-(6-deoxy-6-phosphono-beta-D-allofuranosyl)-5-(2-(E)-phenylvinyl)-cytosine
sitting drop vapour diffusion method with 1.8 M of MgSO4 and 0.1 M of Tris, pH 8.5
-
soluble form of human soluble CD73 at 2.2 A resolution, a truncated form of CD73, residues 27–549, that retains ecto-5'-nucleotidase activity. Structure reveals a conserved loop that is directly involved in the dimer-dimer interaction showing that the two subunits of the dimer are not linked by disulfide bridges
in complex with phosphate and GMP, to 2.7 A nd 2.5 A resolution, respectively. Structures reveal an activator-binding site at the dimer interface
X-ray structure of catalytically inactivate variant D51N of murine cN-III with substrate uridine 5'-monophosphate at 1.74 A resolution. The aromatic ring of a nitrogenous base of the substrate nucleotide is stabilized by parallel pi-stacking interactions with conserved aromatic rings of Trp113 and His68. The nitrogenous base is further stabilized by T-shaped stacking with the conserved aromatic ring of Tyr114, as well as by polar contacts with side chains of Thr66 and Ser117. Two water molecules help to stabilize the nucleotide binding by bridging it to protein residues Asp72 and His68 via hydrogen bonds. Glu96 is responsible for recognition of ribose ring via two hydrogen bonds