Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae NEM316

Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid

Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the NAD ⁺-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate and its reverse reaction in glycolysis and gluconeogenesis.

Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase ( HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells.

Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein ( HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies of HsGAPDH across three of the crystal forms obtained is 0.31±0.17.

Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result in HsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.

Partial catalytic Cys oxidation of human GAPDH

Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the reversible NAD+-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate in both glycolysis and gluconeogenesis.Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase (HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells.Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein (HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies ofHsGAPDH across three of the crystal forms obtained is 0.31±0.17.Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result inHsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.

Analyzing the adhesion mechanism of FnBPA, a surface adhesin from Staphylococcus aureus on its interaction with nanoparticle

Staphylococcus aureus expresses many Microbial Surface Recognizing Adhesive Matrix Molecules (MSCRAMM's) to recognize host extracellular matrix (ECM) molecules to initiate colonization. The MSCRAMM, fibronectin binding protein A (FnBPA), is an important adhesin for S. aureus infection. FnBPA also binds with fibrinogen (Fg) by using a unique ligand binding mechanism called dock, lock and latch. Nanoparticles, especially nanosilver particles have been widely used in a variety of biomedical applications which includes disease diagnosis and treatment, drug delivery and implanted medical device coating. In a biological system, when protein molecules encounter nanoparticle, they can be absorbed onto its surface which results in the formation of protein corona. In the present study, we have analysed the fibrinogen binding ability of rFnBPA_(189-512) in the presence of silver nanoparticles by employing techniques like gel shift assay, Western blot, size exclusion chromatography, enzyme-linked immunosorbent assay, bio-layer interferometry and circular dichroism spectroscopy. The results indicate that rFnBPA_(189-512) is unable to bind to Fg in the presence of a nanoparticle. This could be due to the inaccessibility of the Fg binding site and conformational change in rFnBPA_(189-512). With nanoparticles, rFnBPA_(189-512) undergoes significant structural changes as the β-sheet content has drastically reduced to 10% from the initial 60% at higher concentration of the nanoparticle. Pathogenic bacteria interact with its surrounding environment through their surface molecules which includes MSCRAMMs. Therefore MSCRAMMs play an important role when bacteria encounter nanoparticles. The results of the present study suggest that the orientation of the protein during the absorption on the surface of a nanoparticle as well as the concentration of the nanoparticle, will dictate the function of the absorbed protein and in this case the Fg binding property of rFnBPA_(189-512).

Crystal structure of GAPDH of Streptococcus agalactiae and characterization of its interaction with extracellular matrix molecules

GAPDH being a key enzyme in the glycolytic pathway is one of the surface adhesins of many Gram-positive bacteria including Streptococcus agalactiae. This anchorless adhesin is known to bind to host plasminogen (PLG) and fibrinogen (Fg), which enhances the virulence and modulates the host immune system. The crystal structure of the recombinant GAPDH from S. agalactiae (SagGAPDH) was determined at 2.6 Å resolution by molecular replacement. The structure was found to be highly conserved with a typical NAD binding domain and a catalytic domain. In this paper, using biolayer interferometry studies, we report that the multifunctional SagGAPDH enzyme binds to a variety of host molecules such as PLG, Fg, laminin, transferrin and mucin with a K_D value of 4.4 × 10^-7 M, 9.8 × 10^-7 M, 1 × 10^-5 M, 9.7 × 10^-12 M and 1.4 × 10^-7 M respectively. The ligand affinity blots reveal that SagGAPDH binds specifically to α and β subunits of Fg and the competitive binding ELISA assay reveals that the Fg and PLG binding sites on GAPDH does not overlap each other. The PLG binding motif of GAPDH varies with organisms, however positively charged residues in the hydrophobic surroundings is essential for PLG binding. The lysine analogue competitive binding assay and lysine succinylation experiments deciphered the role of SagGAPDH lysines in PLG binding. On structural comparison with S. pneumoniae GAPDH, K171 of SagGAPDH is being predicted to be involved in PLG binding. Further SagGAPDH exhibited enzymatic activity in the presence of Fg, PLG and transferrin. This suggests that these host molecules does not mask the active site and bind at some other region of GAPDH.

Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294-307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.