Candidatus Liberibacter asiaticus (CLas) is a host-dependent obligate bacteria that causes citrus greening disease in citrus plants. The prolonged association of CLas with the host led to the loss of essential metabolic genes, including transaldolase in the pentose phosphate pathway, hindering the development of axenic culture in the host-free environment. In this study, in silico functional annotation of pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP) protein was performed by utilizing sequence analysis and molecular modeling, revealing its potential role in bypassing the loss of transaldolase. The findings suggest how PFP and fructose bisphosphate aldolase (FBPA) can reconstruct the disrupted central carbon metabolism and help CLas in ATP production. The molecular modeling of PFP showed binding affinity towards fructose 6-phosphate and sedoheptulose 7-phosphate, showing its dual function. The sequence-based analysis and metabolic modeling study also highlight the presence of other alternate enzymes or transport proteins in CLas, elucidating the broader metabolic resilience. This is the first report to provide the structural insights of PFP in compensating for the lost metabolic function and survival strategies adopted by CLas despite the restrained metabolic capability.