Structure-Function Analysis Glyceraldehyde-3-Phosphate Dehydrogenase Homologue GapB in Staphylococcus aureus

Abstract

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is the most studied reference protein that catalysis the inter-conversion reaction of glyceraldehyde-3-phosphate into 1,3-diphosphoglycerate using NAD+ as coenzyme. GAPDH is also recognized as an important player in DNA repair mechanisms, autophagic and apoptotic cell deaths and posttranslational modifications. Staphylococcus aureus is Gram positive commensal pathogenic bacteria. In the genome of S. aureus, GapA was assumed to be a glycolytic GAPDH and GapB was assumed to be a gluconeogenic GAPDH. The crystal structure of GapA has already been in preceding studies. However, to my knowledge, no structural studies on the gapB homologue is available in the literature. The main aims of this study were to analyze physicochemical properties and generate a homology model structure of GAPDH homologue GapB in S. aureus. This was carried out by Protparam tool, Phyre2 homology modeling server and PSIPRED secondary structure analysis tool. ProtParam predicted that GapB is a stable and liposoluble protein. Homology modeling studies revealed that each subunit of GapB was made up by two domains: the NAD coenzyme binding-domain and the catalytic domain. The NAD binding domain was shown to contain a Rossman fold. On the other hand, the catalytic domain was made up by a mixture of eight strands of beta sheet and seven alfa helices. PSIPRED analysis revealed that the secondary structure of the GapB contains α-helices (29.91%), extended strands (24.63%) and random coil (45.45%).