4NWI

Crystal structure of cytosolic 5'-nucleotidase IIIB (cN-IIIB) bound to cytidine

Summary for 4NWI

• Entry DOI: 10.2210/pdb4nwi/pdb
• Related: 4NV0
• Descriptor: 7-methylguanosine phosphate-specific 5'-nucleotidase, MAGNESIUM ION, 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE, ... (5 entities in total)
• Functional Keywords: rossmannoid fold, 5'-nucleotidase, hydrolase
• Biological source: Drosophila melanogaster (Fruit fly)
• Total number of polymer chains: 2
• Total formula weight: 73282.16

Authors

Monecke, T.,Neumann, P.,Ficner, R. (deposition date: 2013-12-06, release date: 2014-03-19, Last modification date: 2023-11-08)

Primary citation

Monecke, T.,Buschmann, J.,Neumann, P.,Wahle, E.,Ficner, R.
Crystal Structures of the Novel Cytosolic 5'-Nucleotidase IIIB Explain Its Preference for m7GMP
Plos One, 9:e90915-e90915, 2014

PubMed Abstract: 5'-nucleotidases catalyze the hydrolytic dephosphorylation of nucleoside monophosphates. As catabolic enzymes they contribute significantly to the regulation of cellular nucleotide levels; misregulation of nucleotide metabolism and nucleotidase deficiencies are associated with a number of diseases. The seven human 5'-nucleotidases differ with respect to substrate specificity and cellular localization. Recently, the novel cytosolic 5'-nucleotidase III-like protein, or cN-IIIB, has been characterized in human and Drosophila. cN-IIIB exhibits a strong substrate preference for the modified nucleotide 7-methylguanosine monophosphate but the structural reason for this preference was unknown. Here, we present crystal structures of cN-IIIB from Drosophila melanogaster bound to the reaction products 7-methylguanosine or cytidine. The structural data reveal that the cytosine- and 7-methylguanine moieties of the products are stacked between two aromatic residues in a coplanar but off-centered position. 7-methylguanosine is specifically bound through π-π interactions and distinguished from unmodified guanosine by additional cation-π coulomb interactions between the aromatic side chains and the positively charged 7-methylguanine. Notably, the base is further stabilized by T-shaped edge-to-face stacking of an additional tryptophan packing perpendicularly against the purine ring and forming, together with the other aromates, an aromatic slot. The structural data in combination with site-directed mutagenesis experiments reveal the molecular basis for the broad substrate specificity of cN-IIIB but also explain the substrate preference for 7-methylguanosine monophosphate. Analyzing the substrate specificities of cN-IIIB and the main pyrimidine 5'-nucleotidase cN-IIIA by mutagenesis studies, we show that cN-IIIA dephosphorylates the purine m7GMP as well, hence redefining its substrate spectrum. Docking calculations with cN-IIIA and m7GMP as well as biochemical data reveal that Asn69 does not generally exclude the turnover of purine substrates thus correcting previous suggestions.

PubMed: 24603684
DOI: 10.1371/journal.pone.0090915

Experimental method

X-RAY DIFFRACTION (2.05 Å)