The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs

Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, SmPNP2. Thermofluorescence screening of different ligands suggested cytidine and cytosine are potential ligands. The binding of cytosine and cytidine were confirmed by isothermal titration calorimetry, with a K_D of 27 μM for cytosine, and a K_M of 76.3 μM for cytidine. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystal structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capacity of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site thus permitting an alternative binding mode for nucleosides, with a 180° rotation from the canonical binding mode. The remarkable plasticity of this binding site enhances our understanding of the correlation between structure and nucleotide selectivity, thus suggesting new ways to analyse PNP activity.

Transient expression in HEK 293 cells: an alternative to E. coli for the production of secreted and intracellular mammalian proteins

Transient transfection of human embryonic kidney cells (HEK 293) enables the rapid and affordable lab-scale production of recombinant proteins. In this chapter protocols for the expression and purification of both secreted and intracellular proteins using transient expression in HEK 293 cells are described.

Crystal structure of Schistosoma mansoni HGPRT isoform 1

Schistosoma mansoni is the parasite responsible for schistosomiasis, a disease that affects about 207 million people worldwide [1], and does not have the purine "de novo" pathway, depending entirely on the purine salvage pathway to supply its demands on purines [2]. The purine salvage pathway has been reported as a potential target for developing new drugs against schistosomiasis. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a key enzyme in this pathway and the only validated enzyme target of the pathway [3]. HGPRT catalyzes the PRPP dependent conversion of hypoxanthine/guanine to inosine monophosphate or guanine to guanosine monophosphate. HGPRT1 gene was amplified, cloned, expressed and purified at the Oxford Protein Production Facility (OPPF-UK). Robotic crystallization trials were performed and SmHGPRT crystallized in several conditions of the Morpheus crystallization kit: A4, A8, A9, and C9. The crystals appear about a day and have about 30 μM in greatest dimension. About a hundred crystals were screened with x-rays on the macromolecular crystallography beamlines I02 and I24 at Diamond Light Source. 21 datasets was collected from 2.97 to 4.11Å resolution. A solution was obtained for HGPRT1 belongs space group P212121 in a dataset to 3.4Å resolution, with four monomer in the ASU. The structure was solved by the program Phaser using HGPRT human as a search model. The refinement is being carried out by program Phenix. The density map is acceptable for the resolution but a great manual work of interpretation is necessary for the refinement of this structure. The most important is the demonstration that it was possible to crystallize and collect data of SmHGPRT. A major effort will be undertaken to improve the size and diffraction power of HGPRT crystals as well as in the resolution of the structure of HGPRT in other space groups. This structure will increase the structural information available about the Schistosoma mansoni purine salvage pathway.

S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA

The putative methyltransferase CmoA is involved in the nucleoside modification of transfer RNA. X-ray crystallography and mass spectrometry are used to show that it contains a novel SAM derivative, S-adenosyl-S-carboxymethyl-l-homocysteine, in which the donor methyl group is replaced by a carboxymethyl group.

Uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo⁵U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo⁵U and was annotated as an S-adenosyl-l-methionine-dependent (SAM-dependent) methyltransferase on the basis of its sequence homology to other SAM-containing enzymes. However, both the crystal structure of Escherichia coli CmoA at 1.73 Å resolution and mass spectrometry demonstrate that it contains a novel cofactor, S-adenosyl-S-carboxymethyl-l-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxy­methyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other SAM-containing enzymes. This raises the possibility that a number of enzymes that have previously been annotated as SAM-dependent are in fact SCM-SAH-dependent. Indeed, inspection of electron density for one such enzyme with known X-­ray structure, PDB entry 1im8, suggests that the active site contains SCM-SAH and not SAM.

Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118

The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.