Streptococcus pneumoniae (pneumococcus) infection claims more than 1.6 million deaths worldwide. Capsular polysaccharides (CPS) are major virulence factors by protecting pneumococci from host. Synthesis of CPS requires energy supplied by ATP hydrolysis, and adenylate kinases (AdKs) constitute a major family of enzymes to regulate cellular ATP level. However, it remains poorly understood whether AdK acts as a virulence factor in pneumococcal diseases. Here we show that AdK from S. pneumoniae (SpAdK) is essential for growth and CPS synthesis by crystallographic and functional studies. We determined the crystal structure of SpAdK in two conformations: ligand-free open form and closed in complex with a two-substrate mimic inhibitor adenosine pentaphosphate (Ap5A). Arginine-89 (Arg-89) was identified as the key active site residue, suppressing pneumococcal growth both in non-encapsulated and encapsulated strains when mutated. We generated a conditional expression mutant of pneumococcus, in which the expression of the adk gene is tightly regulated by fucose. Expression of the wild-type adk gene in fucose-inducible strains rescued growth defect, but expression of the Arg-89 mutation did not. Cellular ATP and CPS levels were increased in proportion to the expression level of adk gene. Consistently, pneumococcal resistance to phagocytosis by macrophages was also increased by SpAdK expression. Taken together, our results support that SpAdK is required for pneumococcal growth and CPS systhesis via its enzymatic activity and renders S. pneumoniae resistant to phagocytosis. We propose that SpAdK is a novel pneumococcal virulence factor.